WorldWideScience

Sample records for chemically structured pigments

  1. Nanoscale porosity in pigments for chemical sensing

    OpenAIRE

    Kemling, Jonathan W.; Suslick, Kenneth S.

    2011-01-01

    Porous pigments in which chemically responsive dyes have been immobilized in a matrix of organically modified siloxanes (ormosils) have been prepared and characterized by AFM, TEM, EDS, and optical analysis. In typical chemical sensing applications, an array of 36 different porous ormosil pigments are deposited on polyethylene terephthalate (PET) film.

  2. Nanoscale porosity in pigments for chemical sensing.

    Science.gov (United States)

    Kemling, Jonathan W; Suslick, Kenneth S

    2011-05-01

    Porous pigments in which chemically responsive dyes have been immobilized in a matrix of organically modified siloxanes (ormosils) have been prepared and characterized by AFM, TEM, EDS, and optical analysis. In typical chemical sensing applications, an array of 36 different porous ormosil pigments are deposited on polyethylene terephthalate (PET) film.

  3. SYNTHESIS OF PLASTIC PIGMENT WITH MULTIHOLLOW STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    Liqiang Jin; Qinghua Xu; Zonglin Liu

    2004-01-01

    The polymer particle possessing hollow structure are playing an increasingly important role in industry.The latex particle with hollow structure as plastic pigment has a low density, strong spreading capacity and good glossiness. So it has been utilized for the manufacture of LWC in paper-making. In this paper,we prepared a kind of novel plastic pigment by the soapless seeded emulsion polymerization, this product with polyacrylate as core and with polystyrene as shell (PA/PS) had hollow structure after dryness. The preparation, characterization and properties of the latex were studied in detail by chemistry analysis and apparatus analysis such as TEM,FTIR,DLS.

  4. SYNTHESIS OF PLASTIC PIGMENT WITH MULTIHOLLOW STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    LiqiangJin; QinghuaXu; ZonglinLiu

    2004-01-01

    The polymer particle possessing hollow structure are playing an increasingly important role in industry. The latex particle with hollow structure as plastic pigment has a low density, strong spreading capacity and good glossiness. So it has been utilized for the manufacture of LWC in paper-making. In this paper, we prepared a kind of novel plastic pigment by the soapless seeded emulsion polymerization, this product with polyacrylate as core and with polystyrene as shell (PA/PS) had hollow structure after dryness. The preparation, characterization and properties of the latex were studied in detail by chemistry analysis and apparatus analysis such as TEM,FTIR,DLS.

  5. Chemical purity and toxicology of pigments used in tattoo inks.

    Science.gov (United States)

    Petersen, Henrik; Lewe, Dirk

    2015-01-01

    The safety of tattoo inks has obviously increased in Europe since the existence of European Union Resolution ResAP(2008)1, which resulted in the improved quality control of pigment raw materials due to the definition of impurity limits that manufacturers can refer to. High-performance pigments are mostly used in tattoo inks, and these pigments are supposed to be chemically inert and offer high light fastness and low migration in solvents. However, these pigments were not developed or produced for applications involving long-term stay in the dermis or contact with bodily fluids. Therefore, these pigments often do not comply with the purity limits of the resolution; however, it is required that every distributed tattoo ink does not contain aromatic amines and not exceed the limits of heavy metals or polycyclic aromatic hydrocarbons. Current toxicity studies of pigments underline that no ecotoxicological threat to human health or to the environment should be expected. However, the pigment as well as its impurities and coating materials must be considered. In order to evaluate the safety of pigments according to their impurities, two different validated sample preparation methods are necessary: (1) simulation of their long-term stay in the bodily fluid of the dermis and (2) simulation of cleavage due to laser removal or ultraviolet exposure. The development of standardized, validated and well-adapted methods for this application has to be part of prospective efforts. Concerning legislation, it might be appropriate that the first regulative approaches be based on those of cosmetics.

  6. Chemically responsive nanoporous pigments: colorimetric sensor arrays and the identification of aliphatic amines.

    Science.gov (United States)

    Bang, Jin Ho; Lim, Sung H; Park, Erwin; Suslick, Kenneth S

    2008-11-18

    A general method has been developed for the preparation of microspheres of nanoporous pigments, their formulation into chemically responsive pigment inks, and the printing of these inks as colorimetric sensor arrays. Using an ultrasonic-spray aerosol-gel synthesis from chemically responsive dyes and common silica precursors, 16 different nanoporous pigment microspheres have been prepared and characterized. New colorimetric sensor arrays have been created by printing inks of these chemically responsive pigments as primary sensor elements; these arrays have been successfully tested for the detection, identification, and quantitation of toxic aliphatic amines. Among 11 structurally similar amines, complete identification of each analyte without confusion was achieved using hierarchical cluster analysis (HCA). Furthermore, visual identification of ammonia gas was easily made at the IDLH (immediately dangerous to life or health), PEL (permissible exposure limits), and 0.1 PEL concentrations with high reproducibility.

  7. Colloidal assembly in Leidenfrost drops for noniridescent structural color pigments.

    Science.gov (United States)

    Lim, Che Ho; Kang, Hyelim; Kim, Shin-Hyun

    2014-07-22

    Noniridescent structural color pigments have great potential as alternatives to conventional chemical color pigments in many coloration applications due to their nonbleaching and color-tunable properties. In this work, we report a novel method to create photonic microgranules composed of glassy packing of silica particles and small fraction of carbon black nanoparticles, which show pronounced structural colors with low angle-dependency. To prepare isotropic random packing in each microgranule, a Leidenfrost drop, which is a drop levitated by its own vapor on a hot surface, is employed as a template for fast consolidation of silica particles. The drop randomly migrates over the hot surface and rapidly shrinks, while maintaining its spherical shape, thereby consolidating silica particles to granular structures. Carbon black nanoparticles incorporated in the microgranules suppress incoherent multiple scattering, thereby providing improved color contrast. Therefore, photonic microgranules in a full visible range can be prepared by adjusting the size of silica particles with insignificant whitening.

  8. Chemical research on red pigments after adverse reactions to tattoo.

    Science.gov (United States)

    Tammaro, A; Toniolo, C; Giulianelli, V; Serafini, M; Persechino, S

    2016-03-01

    Currently, the incidence of tattooing is on the rise compared to the past, especially among adolescents, and it leads to the urgency of monitoring the security status of tattooing centers, as well as to inform people about the risks of tattoo practice. In our clinical experience, 20% of tattooed patients presented adverse reactions, like allergic contact dermatitis, psoriasis with Koebner's phenomena and granulomatous reactions, with the latter most prevalent and most often related to red pigment. Adverse reactions to tattoo pigments, especially the red one, are well known and described in literature. Great attention has to be focused on the pigments used, especially for the presence of new substances, often not well known. For this reason, we decided to perform a study on 12 samples of red tattoo ink, obtained by patients affected by different cutaneous reactions in the site of tattoo, to analyze their chemical composition.

  9. Tertiary structure and spectral tuning of UV and violet pigments in vertebrates

    Science.gov (United States)

    Yokoyama, Shozo; Starmer, William T.; Takahashi, Yusuke; Tada, Takashi

    2010-01-01

    Many vertebrate species use ultraviolet (UV) vision for such behaviors as mating, foraging, and communication. UV vision is mediated by UV-sensitive visual pigments, which have the wavelengths of maximal absorption (λmax) at ~360 nm, whereas violet (or blue) vision is mediated by orthologous pigments with λmax values of 390–440 nm. It is widely believed that amino acids in transmembrane (TM) I–III are solely responsible for the spectral tuning of these SWS1 pigments. Recent molecular analyses of SWS1 pigments, however, show that amino acids in TM IV–VII are also involved in the spectral tuning of these pigments through synergistic interactions with those in TM I–III. Comparisons of the tertiary structures of UV and violet pigments reveal that the distance between the counterion E113 in TM III and amino acid sites 87–93 in TM II is narrower for UV pigments than for violet pigments, which may restrict the access of water molecules to the Schiff base pocket and deprotonate the Schiff base nitrogen. Both mutagenesis analyses of E113Q and quantum chemical calculations strongly suggest that unprotonated Schiff base-linked chromophore is responsible for detecting UV light. PMID:16343816

  10. The challenges and limitations of chemical analysis of particulate pigments of very low solubility.

    Science.gov (United States)

    Olsen, Ole

    2015-01-01

    When performing a chemical analysis of colorants in tattoo products, specific degradation products as well as impurity patterns can be predicted. Mislabeling or false declarations can also be avoided using this test. It is notable that pigment identification in tattoo products may serve as a precursory technique to recognize the colorants contained in a patient's tattoo prior to laser removal therapy. In contrast to the analysis of banned pigments, positive identification of pigments will normally require few reference substances. Given the fact that tattoo pigments are nearly insoluble in water and many organic solvents, different chemical pigment analyses are outlined and evaluated. Related publications from the study of art are also mentioned. It is recommended that access to comprehensive pigment standards and spectroscopic databanks should be offered to laboratories dealing with tattoo product analysis in the future.

  11. The ascidian pigmented sensory organs: structures and developmental programs.

    Science.gov (United States)

    Esposito, R; Racioppi, C; Pezzotti, M R; Branno, M; Locascio, A; Ristoratore, F; Spagnuolo, A

    2015-01-01

    The recent advances on ascidian pigment sensory organ development and function represent a fascinating platform to get insight on the basic programs of chordate eye formation. This review aims to summarize current knowledge, at the structural and molecular levels, on the two main building blocks of ascidian light sensory organ, i.e. pigment cells and photoreceptor cells. The unique features of these structures (e.g., simplicity and well characterized cell lineage) are indeed making it possible to dissect the developmental programs at single cell resolution and will soon provide a panel of molecular tools to be exploited for a deep developmental and comparative-evolutionary analysis.

  12. Production and chemical characterization of pigments in filamentous fungi.

    Science.gov (United States)

    Souza, Patrícia Nirlane da Costa; Grigoletto, Tahuana Luiza Bim; de Moraes, Luiz Alberto Beraldo; Abreu, Lucas M; Guimarães, Luís Henrique Souza; Santos, Cledir; Galvão, Luciano Ribeiro; Cardoso, Patrícia Gomes

    2016-01-01

    Production of pigments by filamentous fungi is gaining interest owing to their use as food colourants, in cosmetics and textiles, and because of the important biological activities of these compounds. In this context, the objectives of this study were to select pigment-producing fungi, identify these fungi based on internal transcribed spacer sequences, evaluate the growth and pigment production of the selected strains on four different media, and characterize the major coloured metabolites in their extracts. Of the selected fungal strains, eight were identified as Aspergillus sydowii (CML2967), Aspergillus aureolatus (CML2964), Aspergillus keveii (CML2968), Penicillium flavigenum (CML2965), Penicillium chermesinum (CML2966), Epicoccum nigrum (CML2971), Lecanicillium aphanocladii (CML2970) and Fusarium sp. (CML2969). Fungal pigment production was influenced by medium composition. Complex media, such as potato dextrose and malt extract, favoured increased pigment production. The coloured compounds oosporein, orevactaene and dihydrotrichodimerol were identified in extracts of L. aphanocladii (CML2970), E. nigrum (CML2971), and P. flavigenum (CML2965), respectively. These results indicate that the selected fungal strains can serve as novel sources of pigments that have important industrial applications.

  13. Structures and colour properties of new red wine pigments

    DEFF Research Database (Denmark)

    Håkansson, Anders Eckart; Pardon, K.; Hayasaka, Y.;

    2003-01-01

    Two new red pigments were synthesized by nucleophilic addition of vinylphenols to malvidin 3-glucoside. The structures of the resulting pyranoanthocyanins were confirmed by electrospray-mass spectrometry and NMR spectroscopy (gHMQC gHMBC and CIGAR experiments). By means of UV-vis spectroscopy...

  14. Antibiotic pigment from desert soil actinomycetes; biological activity, purification and chemical screening

    Directory of Open Access Journals (Sweden)

    Selvameenal L

    2009-01-01

    Full Text Available An actinomycete strain, Streptomyces hygroscopicus subsp. ossamyceticus (strain D10 was isolated from Thar Desert soil, Rajasthan during the year 2006 and found to produce a yellow color pigment with antibiotic activity. Crude pigment was produced from strain D10 by solid state fermentation using wheat bran medium followed by extraction with ethyl acetate. The antimicrobial activity of the crude pigment was evaluated against drug resistant pathogens such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant Staphylococcus aureus, extended spectrum b-lactamase producing cultures of Escherichia coli, Pseudomonas aeruginosa and Klebsiella sp. About 420 mg of crude pigment was produced per 10 g of wheat bran medium. In the disc diffusion method the crude ethyl acetate extract showed a minimum of 10 mm inhibition against Klebsiella sp. and maximum of 19 mm of inhibition against Escherichia coli. The crude pigment was partially purified using thin layer chromatography with the solvent system chloroform:methanol (30:70 and the Rf value was calculated as 0.768. Antimicrobial activity of the partially purified compound from thin layer chromatography was determined using the bioautography method. The purified pigment showed minimum of 15 mm inhibition against Klebsiella sp. and a maximum of 23 mm of inhibition against vancomycin-resistant Staphylococcus aureus in the disc diffusion method. Based on the results of chemical screening, the pigment was tentatively identified as group of sugar containing molecules.

  15. Enhancing the chroma of pigmented polymers using antireflective surface structures

    DEFF Research Database (Denmark)

    Clausen, Jeppe Sandvik; Christiansen, Alexander Bruun; Kristensen, Anders;

    2013-01-01

    In this paper we investigate how the color of a pigmented polymer is affected by reduction of the reflectance at the air-polymer interface. Both theoretical and experimental investigations show modified diffuse-direct reflectance spectra when the reflectance of the surface is lowered. Specifically...... it is found that the color change is manifested as an increase in chroma, leading to a clearer color experience. The experimental implementation is done using random tapered surface structures replicated in polymer from silicon masters using hot embossing....

  16. Finding Hidden Chemistry in Ancient Egyptian Artifacts: Pigment Degradation Taught in a Chemical Engineering Course

    Science.gov (United States)

    Gime´nez, Javier

    2015-01-01

    The main objective of this work was to show the application of the study of ancient technology and science on teaching (and learning) chemistry in Chemical Engineering Undergraduate studies. Degradation patterns of pigments used in Ancient Egypt were incorporated in the syllabus of the course entitled "Technological and Scientific…

  17. Finding Hidden Chemistry in Ancient Egyptian Artifacts: Pigment Degradation Taught in a Chemical Engineering Course

    Science.gov (United States)

    Gime´nez, Javier

    2015-01-01

    The main objective of this work was to show the application of the study of ancient technology and science on teaching (and learning) chemistry in Chemical Engineering Undergraduate studies. Degradation patterns of pigments used in Ancient Egypt were incorporated in the syllabus of the course entitled "Technological and Scientific…

  18. Carotenoid:β-cyclodextrin stability is independent of pigment structure.

    Science.gov (United States)

    Fernández-García, Elisabet; Pérez-Gálvez, Antonio

    2017-04-15

    Carotenoids refer to a wide class of lipophilic pigments synthesized by plants, exert photoprotective and antioxidant properties that are lost upon carotenoid degradation. Their inclusion into hydrophilic host-molecules could improve their stability. Cyclodextrins, provide a hydrophobic cavity in the core of their structure while the outer configuration is suitable with aqueous environments. Carotenoids can accommodate into the hydrophobic core of cyclodextrins and therefore, they are protected from exogenous stress. Literature reported that carotenoid structure could modulate stability of the complexes, however no conclusions can be drawn as the studies performed so far were not completely analogous. We describe the synthesis of several carotenoids/β-CDs inclusion complexes and provide experimental evidences that β-CDs inclusion renders these compounds more stability towards the oxidizing agents (2,2'-azobis, 2-methylpropionamidine dihydrochloride and hydrogen peroxide). Esterified carotenoids were also used in this work to screen the influence of this particular structural configuration of xanthophylls against oxidation.

  19. Tattoo inks: legislation, pigments, metals and chemical analysis.

    Science.gov (United States)

    Prior, Gerald

    2015-01-01

    Legal limits for chemical substances require that they are linked to clearly defined analytical methods. Present limits for certain chemicals in tattoo and permanent make-up inks do not mention analytical methods for the detection of metals, polycyclic aromatic hydrocarbons or forbidden colourants. There is, therefore, no established method for the determination of the quantities of these chemicals in tattoo and permanent make-up inks. Failing to provide an appropriate method may lead to unqualified and questionable results which often cause legal disputes that are ultimately resolved by a judge with regard to the method that should have been applied. Analytical methods are tuned to exactly what is to be found and what causes the health problems. They are extremely specific. Irrespective of which is the correct method for detecting metals in tattoo inks, the focus should be on the actual amounts of ink in the skin. CTL® has conducted experiments to determine these amounts and these experiments are crucial for toxicological evaluations and for setting legal limits. When setting legal limits, it is essential to also incorporate factors such as daily consumption, total uptake and frequency of use. A tattoo lasts for several decades; therefore, the limits that have been established for heavy metals used in drinking water or soap are not relevant. Drinking water is consumed on a daily basis and soap is used several times per week, while tattooing only occurs once.

  20. Chemical characterisation of zircon-cadmium sulfoselenide ceramic pigments; Caracterizacion quimica de pigmentos ceramicos a base de sulfoseleniuro de cadmio

    Energy Technology Data Exchange (ETDEWEB)

    Gazulla Barreda, M. F.; Rodrigo Edo, M.; Blasco Roca, E.; Orduna Cordero, M.

    2013-07-01

    The present paper addresses the development of a methodology that allows the complete chemical characterisation of zircon cadmium sulfoselenide ceramic pigments including minor and major elements. To develop the methodology, five zircon-cadmium sulfoselenide pigments with different hues were selected, studying the different measurement process steps, from sample preparation to the optimisation of the measurement of the different components of the pigments by spectroscopic techniques (WD-XRF and elemental analysis by combustion and IR detection). The chemical characterisation method developed was validated with synthetic standards prepared from the mixture of certified reference materials and pure oxides because no certified referenced materials of this type of pigments were commercially available. The developed method can be used for a complete chemical characterization of zircon-cadmium sulfoselenide ceramic pigments with a very low uncertainty for all the elements analysed. (Author)

  1. The chemical synthesis of porphobilinogen an important intermediate of the biosynthesis of the "pigments of life"

    OpenAIRE

    Bobal, Pavel; Neier, Reinhard

    2007-01-01

    Porphobilinogen is the second dedicated intermediate in the biosynthesis of «pigments of life». Only very few alkylpyrroles have been isolated from natural sources so far. The absence of stabilising substituents confers to porphobilinogen a high reactivity. The chemical synthesis of porphobilinogen had to take its sensitivity into account. The published synthesis of this unusual pyrrole are reviewed. The synthetic strategies used are analysed and compared with the biosynthesis.

  2. Structures and colour properties of new red wine pigments

    DEFF Research Database (Denmark)

    Håkansson, Anders Eckart; Pardon, K.; Hayasaka, Y.

    2003-01-01

    the colour properties of the pigments were characterized; it could be demonstrated that the pyranoanthocyanins retained their red colour at pH 3.6 in model wine and were resistant to bisulfite-mediated bleaching. Finally, HPLC-MS analysis confirmed the presence of both anthocyanin-derived pigments in red...... wine....

  3. X-ray texture analysis of paper coating pigments and the correlation with chemical composition analysis

    Science.gov (United States)

    Roine, J.; Tenho, M.; Murtomaa, M.; Lehto, V.-P.; Kansanaho, R.

    2007-10-01

    The present research experiments the applicability of x-ray texture analysis in investigating the properties of paper coatings. The preferred orientations of kaolin, talc, ground calcium carbonate, and precipitated calcium carbonate particles used in four different paper coatings were determined qualitatively based on the measured crystal orientation data. The extent of the orientation, namely, the degree of the texture of each pigment, was characterized quantitatively using a single parameter. As a result, the effect of paper calendering is clearly seen as an increase on the degree of texture of the coating pigments. The effect of calendering on the preferred orientation of kaolin was also evident in an independent energy dispersive spectrometer analysis on micrometer scale and an electron spectroscopy for chemical analysis on nanometer scale. Thus, the present work proves x-ray texture analysis to be a potential research tool for characterizing the properties of paper coating layers.

  4. Full-Spectrum Photonic Pigments with Non-iridescent Structural Colors through Colloidal Assembly

    OpenAIRE

    Park, Jin-Gyu; Kim, Shin-Hyun; Magkiriadou, Sofia; Choi, Tae Min; Kim, Young-Seok; Manoharan, Vinothan N.

    2014-01-01

    Structurally colored materials could potentially replace dyes and pigments in many applications, but it is challenging to fabricate structural colors that mimic the appearance of absorbing pigments. We demonstrate the microfluidic fabrication of “photonic pigments” consisting of microcapsules containing dense amorphous packings of core–shell colloidal particles. These microcapsules show non-iridescent structural colors that are independent of viewing angle, a critical requirement for applicat...

  5. Effects of glycolic acid chemical peeling on facial pigment deposition: evaluation using novel computer analysis of digital-camera-captured images.

    Science.gov (United States)

    Kakudo, Natsuko; Kushida, Satoshi; Suzuki, Kenji; Kusumoto, Kenji

    2013-12-01

    Chemical peeling is becoming increasingly popular for skin rejuvenation in dermatological cosmetic medicine. However, the improvements seen with chemical peeling are often very minor, and it is difficult to conduct a quantitative assessment of pre- and post-treatment appearance. We report the pre- and postpeeling effects for facial pigment deposition using a novel computer analysis method for digital-camera-captured images. Glycolic acid chemical peeling was performed a total of 5 times at 2-week intervals in 23 healthy women. We conducted a computer image analysis by utilizing Robo Skin Analyzer CS 50 and Clinical Suite 2.1 and then reviewed each parameter for the area of facial pigment deposition pre- and post-treatment. Parameters were pigmentation size and four pigmentation categories: little pigmentation and three levels of marked pigmentation (Lv1, 2, and 3) based on detection threshold. Each parameter was measured, and the total area of facial pigmentation was calculated. The total area of little pigmentation and marked pigmentation (Lv1) was significantly reduced. On the other hand, a significant difference was not observed for the total area of marked pigmentation Lv2 and Lv3. This suggests that glycolic acid chemical peeling has an effect on small facial pigment disposition or has an effect on light pigment deposition. As the Robo Skin Analyzer is useful for objectively quantifying and analyzing minor changes in facial skin, it is considered to be an effective tool for accumulating treatment evidence in the cosmetic and esthetic skin field. © 2013 Wiley Periodicals, Inc.

  6. Conjugated polyenes as chemical probes of life signature: use of Raman spectroscopy to differentiate polyenic pigments.

    Science.gov (United States)

    Maia, Lenize F; Fernandes, Rafaella F; Lobo-Hajdu, Gisele; de Oliveira, Luiz F C

    2014-12-13

    Polyenes, which are represented by carotenes, carotenoids and conjugated polyenals, are some of the most important targets for astrobiology, because they can provide strong evidence of the presence of organic compounds in the most extreme environments, such as on Mars. Raman spectroscopy has been used as the main analytical tool in the identification of such compounds, for the greatest variety of living species, from microorganisms to animals and plants. However, using only the position of the characteristic Raman bands can lead to errors in tentatively identifying chemicals. In this work, we present a series of observations that can provide a more complete and robust way to analyse the Raman spectrum of a polyenal, in which the position, the intensity, the use of various laser lines for excitation, and the combination of more than one pigment can be considered in the complete analysis.

  7. Environmental and genetic effects on pigment-based vs. structural component of yellow feather colouration.

    Directory of Open Access Journals (Sweden)

    Jana Matrková

    Full Text Available BACKGROUND: Carotenoid plumage is of widespread use in bird communication. Carotenoid-based feather colouration has recently been shown to be dependent on both pigment concentration and feather structure. If these two components are determined differently, one plumage patch may potentially convey different aspects of individual quality. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the effects of genetic and environmental factors on carotenoid-based yellow breast colouration of Great Tit (Parus major nestlings. By partial cross-fostering, we separated the genetic and pre-natal vs. post-natal parental effects on both the structural and the pigment-based component of carotenoid-based plumage colouration. We also simultaneously manipulated the post-hatching environment by brood size manipulation. The structural component of nestling colouration reflected features of female colouration. On the other hand, the pigment-based component was more affected by rearing conditions presumably representing food quality. While the structural component was related to both origin- and environment-related factors, the pigment-based component seemed to be environment-dependent only. These results support the notion that pigment-based and structural components of feather colouration are determined differently. CONCLUSIONS/SIGNIFICANCE: Chromatic and achromatic components of carotenoid-based feather colouration reflected different aspects of individual quality and history, and thus may potentially form a multicomponent signal.

  8. Spectral tuning of Amazon parrot feather coloration by psittacofulvin pigments and spongy structures.

    Science.gov (United States)

    Tinbergen, Jan; Wilts, Bodo D; Stavenga, Doekele G

    2013-12-01

    The feathers of Amazon parrots are brightly coloured. They contain a unique class of pigments, the psittacofulvins, deposited in both barbs and barbules, causing yellow or red coloured feathers. In specific feather areas, spongy nanostructured barb cells exist, reflecting either in the blue or blue-green wavelength range. The blue-green spongy structures are partly enveloped by a blue-absorbing, yellow-colouring pigment acting as a spectral filter, thus yielding a green coloured barb. Applying reflection and transmission spectroscopy, we characterized the Amazons' pigments and spongy structures, and investigated how they contribute to the feather coloration. The reflectance spectra of Amazon feathers are presumably tuned to the sensitivity spectra of the visual photoreceptors.

  9. Single crystal X-ray structure of the artists' pigment zinc yellow

    Science.gov (United States)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold; Sanyova, Jana; Bendix, Jesper

    2017-08-01

    The artists' pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hitherto been unknown. In this work, zinc yellow was synthesised by precipitation from an aqueous solution of zinc nitrate and potassium chromate under both neutral and basic conditions, and the products were compared with the pigment used in industrial paints. Analyses by Raman microscopy (MRS), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), and powder X-ray diffraction (PXRD), showed that the synthesised products and the industrial pigment were identical. Single-crystal X-ray crystallography determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2- moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type.

  10. Single crystal X-ray structure of the artists’ pigment zinc yellow

    DEFF Research Database (Denmark)

    Simonsen, Kim Pilkjær; Christiansen, Marie Bitsch; Vinum, Morten Gotthold

    2017-01-01

    The artists’ pigment zinc yellow is in general described as a complex potassium zinc chromate with the empirical formula 4ZnCrO4·K2O·3H2O. Even though the pigment has been in use since the second half of the 19th century also in large-scale industrial applications, the exact structure had hithert...... determined the structure of zinc yellow as KZn2(CrO4)2(H2O)(OH) or as KZn2(CrO4)2(H3O2) emphasizing the μ-H3O2 − moiety. Notably, the zinc yellow is isostructural to the recently structurally characterized cadmium analog and both belong to the natrochalcite structure type....

  11. Structural Characterization of Melanin Pigments from Commercial Preparations of the Edible Mushroom Auricularia auricula.

    Science.gov (United States)

    Prados-Rosales, Rafael; Toriola, Stacy; Nakouzi, Antonio; Chatterjee, Subhasish; Stark, Ruth; Gerfen, Gary; Tumpowsky, Paul; Dadachova, Ekaterina; Casadevall, Arturo

    2015-08-26

    Many of the most widely consumed edible mushrooms are pigmented, and these have been associated with some beneficial health effects. Nevertheless, the majority of the reported compounds associated with these desirable properties are non-pigmented. We have previously reported that melanin pigment from the edible mushroom Auricularia auricula can protect mice against ionizing radiation, although no physicochemical characterization was reported. Consequently, in this study we have characterized commercial A. auricula mushroom preparations for melanin content and carried out structural characterization of isolated insoluble melanin materials using a panel of sophisticated spectroscopic and physical/imaging techniques. Our results show that approximately 10% of the dry mass of A. auricula is melanin and that the pigment has physicochemical properties consistent with those of eumelanins, including hosting a stable free radical population. Electron microscopy studies show that melanin is associated with the mushroom cell wall in a manner similar to that of melanin from the model fungus C. neoformans. Elemental analysis of melanin indicated C, H, and N ratios consistent with 5,6-dihydroxyindole-2-carboxylic acid/5,6-dihydroxyindole and 1,8-dihydroxynaphthalene eumelanin. Validation of the identity of the isolated product as melanin was achieved by EPR analysis. A. auricula melanin manifested structural differences, relative to the C. neoformans melanin, with regard to the variable proportions of alkyl chains or oxygenated carbons. Given the necessity for new oral and inexpensive radioprotective materials coupled with the commercial availability of A. auricula mushrooms, this product may represent an excellent source of edible melanin.

  12. Multivariate chemical mapping of pigments and binders in easel painting cross-sections by micro IR reflection spectroscopy.

    Science.gov (United States)

    Rosi, Francesca; Federici, Arianna; Brunetti, Brunetto G; Sgamellotti, Antonio; Clementi, Sergio; Miliani, Costanza

    2011-03-01

    Paintings are composed of superimposed layers of inorganic and organic materials (pigments and binders). Knowledge of the stratigraphic sequence of these heterogeneous layers is fundamental for understanding the artist's painting technique and for conservation issues. In this study, micro-IR mapping experiments in reflection mode have been carried out on cross-sections taken from simulations of ancient easel paintings. The objective was to locate both organic binders and inorganic pigments. Chemical maps have been re-constructed using the common approach based on the integration of specific infrared bands. However, owing to the complexity of painting materials, this approach is not always applicable when dealing with broad and superimposed spectral features and with reststrahlen or derivative-like bands resulting from acquisition in reflection mode. To overcome these limitations, principal-component analysis has been successfully used for the re-construction of the image, extracting the relevant information from the complex full spectral data sets and obtaining reliable chemical distributions of the stratigraphy materials. Different pigment-binder combinations have been evaluated in order to understand limitations and strengths of the approach. Finally, the method has been applied for stratigraphic characterization of a cross-section from a 17th century wooden sculpture identifying both the original paint layer and the several overpaintings constituting the complex stratigraphy.

  13. Tattoo pigments are cleaved by laser light-the chemical analysis in vitro provide evidence for hazardous compounds.

    Science.gov (United States)

    Vasold, Rudolf; Naarmann, Natascha; Ulrich, Heidi; Fischer, Daniela; König, Burkhard; Landthaler, Michael; Bäumler, Wolfgang

    2004-01-01

    In the western world, more than 80 million people decorate their skin with tattoos. Tattoo colorants are injected into the skin, like medical drugs. Most tattoo colorants are industrial pigments, and chemical industries have never produced them for human use but only to stain consumer goods. Up to 10% of tattooed people request removal of their tattoos because of an improved self-image or social stigmatization. In contrast to tattooing, physicians usually perform the tattoo removal. For that purpose laser light at very high intensities irradiates the skin to destroy the tattoo pigments. Based on a recent analysis of tattoo pigments, two widely used azo compounds were irradiated in suspension with laser and subsequently analyzed by using quantitative high-performance liquid chromatography and mass spectrometry. The high laser intensities cleaved the azo compounds, leading to an increase of decomposition products such as 2-methyl-5-nitroaniline, 2-5-dichloraniline and 4-nitro-toluene, which are toxic or even carcinogenic compounds. Moreover, the results of the chemical analysis show that the tattoo colorants already contain such compounds before laser irradiation. Because of a high number of patients undergoing laser treatment of tattoos and based on the results of our findings in vitro, it is an important goal to perform a risk assessment in humans regarding laser-induced decomposition products.

  14. Structure validation in chemical crystallography.

    Science.gov (United States)

    Spek, Anthony L

    2009-02-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

  15. The Crystal Structure of the Malaria Pigment Hemozoin as Elucidated by X-ray Powder Diffraction

    DEFF Research Database (Denmark)

    Straasø, Tine

    in the eradication of malaria. This thesis is a step towards that goal. When examining red blood cells from an infected person under a microscope dark pigment is observed. This dark pigment is actually small crystals called hemozoin. Hemozoin is a by-product formed by the parasite and a necessity for parasitic....... As part of the project an all-in-vacuum powder diffractometer was developed, which provides data with a minimum background level and an improved signal-to-noise ratio. Moreover, the diffractometer is designed with the particular purpose of decreasing the number of parameters to be fitted. Installation...... of the diffractometer at the 60 keV beamline at PETRA III, resulted in data from a diamond powder to unpreceded resolution providing accurate structure factors suitable for advanced electron density modelling....

  16. Crystal structure of Pigment Red 254 from X-ray powder diffraction data

    Directory of Open Access Journals (Sweden)

    Svetlana N. Ivashevskaya

    2017-04-01

    Full Text Available The crystal structure of Pigment Red 254 [P.R. 254, C18H10Cl2N2O2; systematic name: 3,6-bis(4-chlorophenyl-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione] was solved from laboratory X-ray powder diffraction data using the simulated annealing method followed by Rietveld refinement because the very low solubility of the pigment in all solvents impedes the growth of single crystals suitable for X-ray analysis. The molecule lies across an inversion center. The dihedral angle between the benzene ring and the pyrrole ring in the unique part of the molecule is 11.1 (2°. In the crystal, molecules are linked via N—H...O hydrogen bonds, forming chains along [110] incorporating R22(8 rings.

  17. Spatial and temporal variability of the phytoplankton community structure in the North Water Polynya, investigated using pigment biomarkers

    DEFF Research Database (Denmark)

    Vidussi, F.; Roy, S.; Lovejoy, C.

    2004-01-01

    . Autotrophic flagellates dominated in April and May along the Canadian coast, where cold Arctic waters with relatively deep mixed layers were found. In contrast, diatoms dominated in May along the Greenland coast in warmer water masses of Atlantic origin and during June in the whole polynya, except......Phytoplankton taxonomic pigments were measured by high-performance liquid chromatography (HPLC) during a 3-month survey (April-June 1998) in the North Water (NOW) Polynya (Canadian Arctic) to investigate changes in phytoplankton biomass and composition and the physical-chemical factors....... The contribution of the different phytoplankton groups to Chl a inferred using a factorization program (CHEMTAX) indicated that the bloom was diatom-dominated (maximum 94% diatoms). The phytoplankton community structure was influenced by the water mass characteristics and the surface circulation pattern...

  18. Phytoplankton pigments and functional community structure in relation to environmental factors in the Pearl River Estuary

    Directory of Open Access Journals (Sweden)

    Chao Chai

    2016-07-01

    Full Text Available Two cruises were undertaken in the Pearl River Estuary in November 2011 and March 2012 to analyze the distribution of phytoplankton pigments and to define the relationships of pigment indices and functional community structure with environmental factors. Among 22 pigments, 17 were detected by high-performance liquid chromatography. Chlorophyll a was found in all samples, with a maximum of 7.712 μg L−1 in spring. Fucoxanthin was the most abundant accessory pigment, with mean concentrations of 2.914 μg L−1 and 0.207 μg L−1 in spring and autumn, respectively. Chlorophyll a, chlorophyll c2, fucoxanthin, diadinoxanthin, and diatoxanthin were high in the northern or northwest estuary in spring and in the middle-eastern and northeast estuary in autumn. Chlorophyll b, chlorophyll c3, prasinoxanthin, and peridinin were similarly distributed during the two cruises. Chlorophyll a and fucoxanthin positively correlated with nutrients in spring, whereas 19′-hex-fucoxanthin and 19′-but-fucoxanthin negatively correlated. The biomass proportion of microphytoplankton (BPm was higher in spring, whereas that of picophytoplankton (BPp was higher in autumn. BPm in spring was high in areas with salinity 30. BPm increased but BPn reduced with the increase in nutrient contents. By comparison, BPp reduced with the increase in nutrient contents in spring, but no relationship was found between BPp and nutrient contents in autumn. The ratios of photosynthetic carotenoids to photoprotective carotenoids in the southern estuary approached unity linear relationship in spring and were under the unity line in autumn.

  19. Chemical composition, properties, and antimicrobial activity of the water-soluble pigments from Castanea mollissima shells.

    Science.gov (United States)

    You, Ting-Ting; Zhou, Su-Kun; Wen, Jia-Long; Ma, Chao; Xu, Feng

    2014-02-26

    Agricultural residues Castanea mollissima shells represent a promising resource for natural pigments for the food industry. This study provides a comprehensive and systematic evaluation of water-soluble pigments (CSP) from C. mollissima shells, which were obtained by 50% ethanol with microwave-assisted extraction. Spectroscopic techniques (UV, FT-IR, (13)C NMR), elemental analysis, and chromatographic techniques (HPAEC, GPC) revealed that the main components in the CSP were flavonoids procyanidin B3 (condensed tannin), quercetin-3-O-glycoside, and steroidal sapogenins. As a consequence, CSP was water-soluble and presented significant DPPH scavenge capacity (EC50 value was 0.057 mg/mL). Specially, CSP gave excellent antibacterial activity, and even better than 5% aqueous phenol in some case. Moreover, CSP was practically nontoxic and exhibited good stability with temperature, natural light, and metal ions. These outstanding properties will enlarge the application of CSP for natural food additives production.

  20. Structure validation in chemical crystallography

    Science.gov (United States)

    Spek, Anthony L.

    2009-01-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

  1. Effects of Polishing on Proximate Composition, Physico- Chemical Characteristics, Mineral Composition and Antioxidant Properties of Pigmented Rice

    Directory of Open Access Journals (Sweden)

    Chagam Koteswara Reddy

    2017-09-01

    Full Text Available The effects of polishing on proximate compositions, physico-chemical characteristics, mineral compositions and antioxidant properties of the rice flours obtained from three different pigmented rice varieties (Chak-hao Angangba, Chak-hao Amubi and Chak-hao Poireiton were investigated. The rice varieties were significantly (P < 0.05 different in the contents of the test characteristics. Lipids, ash, minerals, phytochemicals (phenolic acids and flavonoids and 2,2-diphenyl-1-picrylhydrazyl (DPPH activity of rice flours were decreased after polishing (9% degree of milling, while amylose content and lightness were increased. X-ray diffraction pattern of rice flours exhibited A-type crystalline pattern with reflections at 15.1°, 17.1°, 18.2° and 23.0°. Pasting properties and transition temperatures were decreased after polishing treatment. Polishing resulted in changes in the crystallinity, enthalpy and morphology of rice flours.

  2. 鸡血藤红色素的提取与基本性质分析%Red Pigment Extraction from Millettia reticulata Benth and Physical and Chemical Properties of Pigment

    Institute of Scientific and Technical Information of China (English)

    许润; 刘建华; 杨广成; 李计龙; 杨迺嘉

    2012-01-01

    探讨鸡血藤红色素的最佳提取溶液,定性定量光、温度、pH值、氧化还原介质对红色素稳定性的影响。结果表明,鸡血藤红色素最佳提取溶剂为65%酸性乙醇(pH1.8),且色素为非花色苷类色素。室内自然光对色素影响不大,该红色素在20~60℃具有较好的稳定性,对氧化剂、还原剂反应敏感。%The red pigment was extracted from Millettia reticulata Benth and the physical and chemical properties of red pigment from Millettia reticulata Benth were investigated, the effects of light, temperature, pH value, oxide-reducing medium on pigment stability were studied. The results showed that the procedure of acid-alcohol extraction gave rather satisfactory results. The pigment does not belong to anthocyanins, and is stable below 20 -- 60 ~C, but its resistance to oxide and reductant is not good.

  3. Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones.

    Science.gov (United States)

    Schmidt, Martin U; Paulus, Erich F; Rademacher, Nadine; Day, Graeme M

    2010-10-01

    The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P2(1)/c, Z = 2, the dichloro derivative in P1, Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P2(1)/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom-atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom-atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph.

  4. Hierarchical structural control of visual properties in self-assembled photonic-plasmonic pigments

    CERN Document Server

    Koay, Natalie; Kay, Theresa M; Nerger, Bryan A; Miles-Rossouw, Malaika; Shirman, Tanya; Vu, Thy L; England, Grant; Phillips, Katherine R; Utech, Stefanie; Vogel, Nicolas; Kolle, Mathias; Aizenberg, Joanna

    2014-01-01

    We present a simple one-pot co-assembly method for the synthesis of hierarchically structured pigment particles consisting of silica inverse-opal bricks that are doped with plasmonic absorbers. We study the interplay between the plasmonic and photonic resonances and their effect on the visual appearance of macroscopic collections of photonic bricks that are distributed in randomized orientations. Manipulating the pore geometry tunes the wavelength- and angle-dependence of the scattering profile, which can be engineered to produce angle-dependent Bragg resonances that can either enhance or contrast with the color produced by the plasmonic absorber. By controlling the overall dimensions of the photonic bricks and their aspect ratios, their preferential alignment can either be encouraged or suppressed. This causes the Bragg resonance to appear either as uniform color travel in the former case or as sparse iridescent sparkle in the later case. By manipulating the surface chemistry of these photonic bricks, which ...

  5. Dye and pigment-free structural colors and angle-insensitive spectrum filters

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Lingjie Jay; Hollowell, Andrew E.; Wu, Yi-Kuei

    2017-01-17

    Optical spectrum filtering devices displaying minimal angle dependence or angle insensitivity are provided. The filter comprises a localized plasmonic nanoresonator assembly having a metal material layer defining at least one nanogroove and a dielectric material disposed adjacent to the metal material layer. The dielectric material is disposed within the nanogroove(s). The localized plasmonic nanoresonator assembly is configured to funnel and absorb a portion of an electromagnetic spectrum in the at least one nanogroove via localized plasmonic resonance to generate a filtered output having a predetermined range of wavelengths that displays angle insensitivity. Thus, flexible, high efficiency angle independent color filters having very small diffraction limits are provided that are particularly suitable for use as pixels for various display devices or for use in anti-counterfeiting and cryptography applications. The structures can also be used for colored print applications and the elements can be rendered as pigment-like particles.

  6. Structure and function of the retinal pigment epithelium, photoreceptors and cornea in the eye of Sardinella aurita (Clupeidae, Teleostei

    Directory of Open Access Journals (Sweden)

    Mostafa Ali Salem

    2016-05-01

    Full Text Available The structure of the pigment epithelium, photoreceptors and the cornea in the eye of a teleost, Sardinella aurita was examined by light and electron microscopy. The retinal pigment epithelium forms a single layer of cells joined laterally by cell junctions. Centrally in the retina these cells are columnar, while more peripherally they become cuboidal in shape. The basal (scleral border of the pigment epithelial cells is not infolded but is relatively smooth. Phagosomes containing lysosome-like bodies are also common features of the retinal pigment epithelium. Numerous melanosomes (pigment granules are abundant throughout the epithelial cells. These melanosomes probably absorb light which has passed through the photoreceptor layer. Four photoreceptor cells were identified; rods, long single cones, short single cones and double cones. The presence of these types suggests a diversity of photoreceptor function. Square mosaic pattern of cones and well-developed choroid gland are also main features of the eye. The inner segment of rods and cones were rich in organelles indicating much synthetic activity. Calycal processes projecting from cone outer segments are also observed. The cornea includes an epithelium with a complex pattern of surface microplicae, a basement membrane, dermal stroma, an iridescent layer, scleral stroma, Descemet’s membrane and endothelium. The autochthonous layer which is seen in some teleosts has not been observed in the cornea of this species. These and other observations were discussed in relation to the photic environment and habits of this fish.

  7. Effect of clinorotation on the leaf mesophyll structure and pigment content in Arabidopsis thaliana L. and Pisum sativum L.

    Science.gov (United States)

    Adamchuk, N I

    2004-07-01

    Properties of mesophyll cells and photosynthetic membranes of Arabidopsis thaliana (L.) Heynh. and Pisum sativum (L.) plants grown in a horizontal clinostat and in control conditions were compared. Obtained data have show that under clinorotation conditions seedlings have experienced the following cell morphology changes structural chloroplast rearrangement in palisade cells, pigment content alteration, and cell aging acceleration.

  8. Can chemical structure predict reproductive toxicity?

    NARCIS (Netherlands)

    Maslankiewicz L; Hulzebos EM; Vermeire TG; Muller JJA; Piersma AH; SEC

    2005-01-01

    Structure-Activity Relationships (SARs), including Quantitative SARs, are applied to the hazard assessment of chemicals. This need is all the more urgent considering the proposed new EU policy on chemicals in REACH, which stresses the need for non-animal testing. DEREKfW and the TSCA Chemical

  9. Unraveling the Electronic Structure of Individual Photosynthetic Pigment-Protein Complexes

    NARCIS (Netherlands)

    Oijen, Antoine M. van; Ketelaars, Martijn; Köhler, Jürgen; Aartsma, Thijs J.; Schmidt, Jan

    1999-01-01

    Low-temperature single-molecule spectroscopic techniques were applied to a light-harvesting pigment-protein complex (LH2) from purple photosynthetic bacteria. The properties of the electronically excited states of the two circular assemblies (B800 and B850) of bacteriochlorophyll a (BChl a) pigment

  10. Unraveling the Electronic Structure of Individual Photosynthetic Pigment-Protein Complexes

    NARCIS (Netherlands)

    Oijen, Antoine M. van; Ketelaars, Martijn; Köhler, Jürgen; Aartsma, Thijs J.; Schmidt, Jan

    1999-01-01

    Low-temperature single-molecule spectroscopic techniques were applied to a light-harvesting pigment-protein complex (LH2) from purple photosynthetic bacteria. The properties of the electronically excited states of the two circular assemblies (B800 and B850) of bacteriochlorophyll a (BChl a) pigment

  11. Environmental and complexation effects on the structures and spectroscopic signatures of organic pigments relevant to cultural heritage: the case of alizarin and alizarin-Mg(II)/Al(III) complexes.

    Science.gov (United States)

    Carta, Luciano; Biczysko, Malgorzata; Bloino, Julien; Licari, Daniele; Barone, Vincenzo

    2014-02-21

    An integrated computational approach allowed an unbiased analysis of optical and structural properties of alizarin-based pigments, which can be directly compared with experimental results. Madder lake pigments have been modeled by Mg(II)- and Al(III)-coordinated alizarin taking into account solvation and metal-linkage effects, responsible for colour modifications. Moreover, different environmental conditions have been analyzed for free alizarin, showing in all cases semi-quantitative agreement with experimental spectroscopic data (UV-VIS). Our results point out the ability of in silico approaches to unravel the subtle interplay of stereo-electronic, dynamic, and environmental effects in tuning the physico-chemical properties of pigments relevant to cultural heritage.

  12. Hyperhomocysteinemia disrupts retinal pigment epithelial structure and function with features of age-related macular degeneration.

    Science.gov (United States)

    Ibrahim, Ahmed S; Mander, Suchreet; Hussein, Khaled A; Elsherbiny, Nehal M; Smith, Sylvia B; Al-Shabrawey, Mohamed; Tawfik, Amany

    2016-02-23

    The disruption of retinal pigment epithelial (RPE) function and the degeneration of photoreceptors are cardinal features of age related macular degeneration (AMD); however there are still gaps in our understanding of underlying biological processes. Excess homocysteine (Hcy) has been reported to be elevated in plasma of patients with AMD. This study aimed to evaluate the direct effect of hyperhomocysteinemia (HHcy) on structure and function of RPE. Initial studies in a mouse model of HHcy, in which cystathionine-β-synthase (cbs) was deficient, revealed abnormal RPE cell morphology with features similar to that of AMD upon optical coherence tomography (OCT), fluorescein angiography (FA), histological, and electron microscopic examinations. These features include atrophy, vacuolization, hypopigmentation, thickened basal laminar membrane, hyporeflective lucency, choroidal neovascularization (CNV), and disturbed RPE-photoreceptor relationship. Furthermore, intravitreal injection of Hcy per se in normal wild type (WT) mice resulted in diffuse hyper-fluorescence, albumin leakage, and CNV in the area of RPE. In vitro experiments on ARPE-19 showed that Hcy dose-dependently reduced tight junction protein expression, increased FITC dextran leakage, decreased transcellular electrical resistance, and impaired phagocytic activity. Collectively, our results demonstrated unreported effects of excess Hcy levels on RPE structure and function that lead to the development of AMD-like features.

  13. Retinal pigment epithelial fine structure in the red-backed salamander (Plethodon cinereus).

    Science.gov (United States)

    Braekevelt, C R

    1992-07-01

    The retinal pigment epithelium (RPE) of the red-backed salamander (Plethodon cinerus) consists of a single layer of large squamous shaped cells. The RPE cells are but minimally infolded basally (sclerally) but show many large apical (vitreal) processes interdigitating with the rod outer segments. These epithelial cells are joined laterally by prominent tight junctions located in the mid region of the cells. Internally smooth endoplasmic reticulum is very plentiful while rough endoplasmic reticulum is not. Polysomes, small dense mitochondria and small round to oval melanosomes are plentiful. Golgi zones and lysosome-like bodies are also present as are phagosomes of outer segment material and myeloid bodies. The RPE cell nucleus is large and vesicular. It is felt that the melanosomes undergo retinomotor movements but as only light-adapted specimens were examined it is not known how extensive are these movements. Bruch's membrane or complexus basalis shows the typical pentalaminate structure noted for most vertebrates. The choriocapillaris is a single layer of large anastomosing capillaries which are minimally fenestrated facing Bruch's membrane.

  14. A simple route to synthesize mesoporous titania from TiOSO4: Influence of the synthesis conditions on the structural, pigments and photocatalytic properties

    Science.gov (United States)

    Yang, Guang; Ding, Hao; Chen, Daimei; Ao, Weihua; Wang, Jian; Hou, Xifeng

    2016-07-01

    The work obtained mesoporous TiO2 white pigments using titanyl sulfate as titanium source with a simple, low-temperature method simplifying the synthesis process and reducing the energy consumption. We investigated the effects of the aging temperature and aging time on the structure and pigments properties of the samples. The structure and morphology of mesoporous samples were characterized by X-ray diffraction and transmission electron microscopy. The obtained mesoporous TiO2 showed excellent pigments properties of whiteness (93.91%), hiding power (12.37 g m-2), and lightness value (97.89), respectively. Moreover, such materials showed outstanding photodegradation performance of organic dyes under UV light irradiation. The current research provided an alternative route to prepare mesoporous TiO2 micspheres white pigments with well photocatalytic performance for indoor purification on industrial scale. It has great significance in titania white pigments field.

  15. Valence-Bond Theory and Chemical Structure.

    Science.gov (United States)

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  16. Physical and Chemical Properties of Black Maize Pigment%黑玉米色素理化性质的研究

    Institute of Scientific and Technical Information of China (English)

    严赞开; 何佶

    2001-01-01

    研究了黑玉米色素的理化性质。结果表明:黑玉米色素可溶于强极性溶剂或稀酸溶液中;色素在酸性介质中呈鲜艳的红色,可见光范围内其特征吸收峰为526 nm;色素对光、热、氧化剂、还原剂、食品添加剂等有较好的稳定性。%The physical and chemical properties of black maize pigment were studied.The results showed that the black maize pigment was soluble in straight polar solvents or in acid medium.The pigment was bright red in acid medium, whose maximum absorption peak was 526 nm .The black maize pigment possessed high stability to light, heat, oxidizing agents, reducing agents and food additives.

  17. A simple route to synthesize mesoporous titania from TiOSO{sub 4}: Influence of the synthesis conditions on the structural, pigments and photocatalytic properties

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Guang; Ding, Hao, E-mail: dinghao113@126.com; Chen, Daimei, E-mail: chendaimei@cugb.edu.cn; Ao, Weihua; Wang, Jian; Hou, Xifeng

    2016-07-15

    Highlights: • A green and facile synthesis of mesoporous TiO{sub 2} is used TiOSO{sub 4} as the Ti source. • This is the first paper to talk about using mesoporous TiO{sub 2} as white pigments. • The obtained materials exhibited well pigments and photocatalytic performance. • Mesoporous TiO{sub 2} may be regarded as an ideal pigments for indoor purification. - Abstract: The work obtained mesoporous TiO{sub 2} white pigments using titanyl sulfate as titanium source with a simple, low-temperature method simplifying the synthesis process and reducing the energy consumption. We investigated the effects of the aging temperature and aging time on the structure and pigments properties of the samples. The structure and morphology of mesoporous samples were characterized by X-ray diffraction and transmission electron microscopy. The obtained mesoporous TiO{sub 2} showed excellent pigments properties of whiteness (93.91%), hiding power (12.37 g m{sup −2}), and lightness value (97.89), respectively. Moreover, such materials showed outstanding photodegradation performance of organic dyes under UV light irradiation. The current research provided an alternative route to prepare mesoporous TiO{sub 2} micspheres white pigments with well photocatalytic performance for indoor purification on industrial scale. It has great significance in titania white pigments field.

  18. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  19. Hydrous non-crystalline phosphates: structure, function and a new white pigment

    OpenAIRE

    ROSSETO, Renato; Santos, Ádamo C. M. A. dos; Galembeck, Fernando

    2006-01-01

    Hydrated non-crystalline inorganic solids are often neglected due to the limited comprehension of their complex physico-chemical and structural properties. However, these non-crystalline materials exhibit a rich and varied chemistry, interesting for scientific and technological reasons. This work reviews general aspects of formation of hydrated non-crystalline solids, with special emphasis on aluminum (poly)phosphate materials. Precursors and concentration variations, temperature, ageing and ...

  20. Diffusion phenomena in chemically stabilized multilayer structures

    NARCIS (Netherlands)

    Bruijn, Saskia

    2011-01-01

    Multilayered thin film structures are widely applied as reflective coatings for optical elements in the extreme ultraviolet wavelength regime. In this thesis we investigate the structural and chemical changes that occur in Mo/Si based multilayers as a result of radiation induced thermal loads and ot

  1. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...

  2. Regulation of Etioplast Pigment-Protein Complexes, Inner Membrane Architecture, and Protochlorophyllide a Chemical Heterogeneity by Light-Dependent NADPH:Protochlorophyllide Oxidoreductases A and B1

    Science.gov (United States)

    Franck, Fabrice; Sperling, Ulrich; Frick, Geneviève; Pochert, Babette; van Cleve, Barbara; Apel, Klaus; Armstrong, Gregory A.

    2000-01-01

    The etioplast of dark-grown angiosperms is characterized by the prolamellar body (PLB) inner membrane, the absence of chlorophyll, and the accumulation of divinyl and monovinyl derivatives of protochlorophyll(ide) a [Pchl(ide) a]. Either of two structurally related, but differentially expressed light-dependent NADPH:Pchlide oxidoreductases (PORs), PORA and PORB, can assemble the PLB and form dark-stable ternary complexes containing enzymatically photoactive Pchlide-F655. Here we have examined in detail whether these polypeptides play redundant roles in etioplast differentiation by manipulating the total POR content and the PORA-to-PORB ratio of etiolated Arabidopsis seedlings using antisense and overexpression approaches. POR content correlates closely with PLB formation, the amounts, spectroscopic properties, and photoreduction kinetics of photoactive Pchlide, the ratio of photoactive Pchlide-F655 to non-photoactive Pchl(ide)-F632, and the ratio of divinyl- to monovinyl-Pchl(ide). This last result defines POR as the first endogenous protein factor demonstrated to influence the chemical heterogeneity of Pchl(ide) in angiosperms. It is intriguing that excitation energy transfer between different spectroscopic forms of Pchl(ide) in etiolated cotyledons remains largely independent of POR content. We therefore propose that the PLB contains a minimal structural unit with defined pigment stoichiometries, within which a small amount of non-photoactive Pchl(ide) transfers excitation energy to a large excess of photoactive Pchlide-F655. In addition, our data suggests that POR may bind not only stoichiometric amounts of photoactive Pchlide, but also substoichiometric amounts of non-photoactive Pchl(ide). We conclude that the typical characteristics of etioplasts are closely related to total POR content, but not obviously to the specific presence of PORA or PORB. PMID:11115885

  3. Monascus pigments.

    Science.gov (United States)

    Feng, Yanli; Shao, Yanchun; Chen, Fusheng

    2012-12-01

    Monascus pigments (MPs) as natural food colorants have been widely utilized in food industries in the world, especially in China and Japan. Moreover, MPs possess a range of biological activities, such as anti-mutagenic and anticancer properties, antimicrobial activities, potential anti-obesity activities, and so on. So, in the past two decades, more and more attention has been paid to MPs. Up to now, more than 50 MPs have been identified and studied. However, there have been some reviews about red fermented rice and the secondary metabolites produced by Monascus, but no monograph or review of MPs has been published. This review covers the categories and structures, biosynthetic pathway, production, properties, detection methods, functions, and molecular biology of MPs.

  4. Chemical structure and dynamics: Annual report 1993

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  5. Melanins: Skin Pigments and Much More—Types, Structural Models, Biological Functions, and Formation Routes

    Directory of Open Access Journals (Sweden)

    F. Solano

    2014-01-01

    Full Text Available This review presents a general view of all types of melanin in all types of organisms. Melanin is frequently considered just an animal cutaneous pigment and is treated separately from similar fungal or bacterial pigments. Similarities concerning the phenol precursors and common patterns in the formation routes are discussed. All melanins are formed in a first enzymatically-controlled phase, generally a phenolase, and a second phase characterized by an uncontrolled polymerization of the oxidized intermediates. In that second phase, quinones derived from phenol oxidation play a crucial role. Concerning functions, all melanins show a common feature, a protective role, but they are not merely photoprotective pigments against UV sunlight. In pathogenic microorganisms, melanization becomes a virulence factor since melanin protects microbial cells from defense mechanisms in the infected host. In turn, some melanins are formed in tissues where sunlight radiation is not a potential threat. Then, their redox, metal chelating, or free radical scavenging properties are more important than light absorption capacity. These pigments sometimes behave as a double-edged sword, and inhibition of melanogenesis is desirable in different cells. Melanin biochemistry is an active field of research from dermatological, biomedical, cosmetical, and microbiological points of view, as well as fruit technology.

  6. Spectral tuning of Amazon parrot feather coloration by psittacofulvin pigments and spongy structures

    NARCIS (Netherlands)

    Tinbergen, Jan; Wilts, Bodo D.; Stavenga, Doekele G.

    2013-01-01

    The feathers of Amazon parrots are brightly coloured. They contain a unique class of pigments, the psittacofulvins, deposited in both barbs and barbules, causing yellow or red coloured feathers. In specific feather areas, spongy nanostructured barb cells exist, reflecting either in the blue or blue-

  7. Water‐soluble red pigments from Isaria farinosa and structural characterization of the main colored component

    DEFF Research Database (Denmark)

    Velmurugan, Palanivel; Lee, Yong Hoon; Nanthakumar, Kuppanan

    2010-01-01

    after treatment with sodium chloride), acid (72.1% with citric acid), heat (86.2% at 60 °C), and sunlight (99.4%). These results are promising to further exploit the fungal culture of Isaria farinosa for producing the red pigment and, subsequently, to considerably increase its yield. The study has...

  8. Structural investigations on betacyanin pigments by LC NMR and 2D NMR spectroscopy.

    Science.gov (United States)

    Stintzing, Florian C; Conrad, Jürgen; Klaiber, Iris; Beifuss, Uwe; Carle, Reinhold

    2004-02-01

    Four betacyanin pigments were analysed by LC NMR and subjected to extensive NMR characterisation after isolation. Previously, low pH values were applied for NMR investigations of betalains resulting in rapid degradation of the purified substances thus preventing extensive NMR studies. Consequently, up to now only one single (13)C NMR spectrum of a betalain pigment, namely that of neobetanin (=14,15-dehydrobetanin), was available. Because of its sufficient stability under highly acidic conditions otherwise detrimental for betacyanins, this pigment remained an exemption. Since betalains are most stable in the pH range of 5-7, a new solvent system has been developed allowing improved data acquisition through improved pigment stability at near neutral pH. Thus, not only (1)H, but for the first time also partial (13)C data of betanin, isobetanin, phyllocactin and hylocerenin isolated from red-purple pitaya [Hylocereus polyrhizus (Weber) Britton & Rose, Cactaceae] could be indirectly obtained by gHSQC- and gHMQC-NMR experiments.

  9. Chemical structure and dynamics. Annual report 1995

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  10. Chemical structure and dynamics: Annual report 1996

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  11. Annual Report 2000. Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  12. The PubChem chemical structure sketcher

    Directory of Open Access Journals (Sweden)

    Ihlenfeldt Wolf D

    2009-12-01

    Full Text Available Abstract PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

  13. Encapsulating betalains from Opuntia ficus-indica fruits by ionic gelation: Pigment chemical stability during storage of beads.

    Science.gov (United States)

    Otálora, María Carolina; Carriazo, José Gregorio; Iturriaga, Laura; Osorio, Coralia; Nazareno, Mónica Azucena

    2016-07-01

    Betalain encapsulation was performed by ionic gelation as a stabilization strategy for these natural pigments. Betalains were extracted from purple cactus fruits and encapsulated in calcium-alginate and in combination of calcium alginate and bovine serum albumin. Beads were characterised by scanning electron microscopy and thermal analysis using differential scanning calorimetry and thermogravimetry. Moisture sorption isotherms were determined. Bead morphology was affected by matrix composition. Pigments storage stability was evaluated at different equilibrium relative humidity and temperatures. Pigment composition of beads was determined by HPLC-MS-MS and degradation products were also analysed after storage; betalamic acid being the major one. Both types of matrices protected the encapsulated pigments, being their storage stability better at low relative humidity than that of the non-encapsulated control material. Antiradical activities of beads were proportional to remaining betalain contents. At high relative humidity, there was no protection and low storage stability was observed in the samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson KWAUK

    2007-01-01

    Around the turn of the present century, scholars began to recognize chemical engineering as a complex system, and have been searching for a convenient point of entry for refreshing its knowledge base. From our study of the dynamic structures of dispersed particles in fluidization and the resulting multi-scale method, we have been attempting to extend our findings to structures prevailing in other multiphase systems as well as in the burgeoning industries producing functional materials. Chemical engineering itself is hierarchically structured. Besides structures based on space and time, such hierarchy could be built from ChE history scaled according to science content, or from ChE operation according to the expenditure of manpower and capital investment.

  15. Analysis and structural characterization of pigments and materials used in Nicolae Grigorescu heritage paintings.

    Science.gov (United States)

    Rusu, R D; Simionescu, B; Oancea, A V; Geba, M; Stratulat, L; Salajan, D; Ursu, L E; Popescu, M C; Dobromir, M; Murariu, M; Cotofana, C; Olaru, M

    2016-11-01

    The combination of various mobile, non-invasive techniques (IR reflectography technique, optical microscopy, XRF, Raman and NIR spectroscopies) and lab-based devices (FTIR and XPS spectroscopies, SEM-EDX microscopy) lead to the first exhaustive investigation of pigments and materials used by the famous Romanian painter Nicolae Grigorescu in three cultural heritage paintings. The study of a large number of spots and samples allowed a rigorous analysis and a far-reaching insight into his work.

  16. Analysis and structural characterization of pigments and materials used in Nicolae Grigorescu heritage paintings

    Science.gov (United States)

    Rusu, R. D.; Simionescu, B.; Oancea, A. V.; Geba, M.; Stratulat, L.; Salajan, D.; Ursu, L. E.; Popescu, M. C.; Dobromir, M.; Murariu, M.; Cotofana, C.; Olaru, M.

    2016-11-01

    The combination of various mobile, non-invasive techniques (IR reflectography technique, optical microscopy, XRF, Raman and NIR spectroscopies) and lab-based devices (FTIR and XPS spectroscopies, SEM-EDX microscopy) lead to the first exhaustive investigation of pigments and materials used by the famous Romanian painter Nicolae Grigorescu in three cultural heritage paintings. The study of a large number of spots and samples allowed a rigorous analysis and a far-reaching insight into his work.

  17. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Lei Chen

    Full Text Available Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer.

  18. Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

    DEFF Research Database (Denmark)

    Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith;

    2016-01-01

    The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... the NH-tautomer with a hydrogen atom situated at the nitrogen of the quinoline moiety. Direct evidence of the presence of the NH-tautomer is provided by 1H–14N HMQC solid-state NMR at very fast MAS. Solid-state dispersion-corrected density functional theory calculations with BLYP-D3 confirm...

  19. Photosynthetic Pigments in Diatoms

    Directory of Open Access Journals (Sweden)

    Paulina Kuczynska

    2015-09-01

    Full Text Available Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

  20. Chemical Structure and Dynamics annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

  1. The blue anthocyanin pigments from the blue flowers of Heliophila coronopifolia L. (Brassicaceae).

    Science.gov (United States)

    Saito, Norio; Tatsuzawa, Fumi; Toki, Kenjiro; Shinoda, Koichi; Shigihara, Atsushi; Honda, Toshio

    2011-12-01

    Six acylated delphinidin glycosides (pigments 1-6) and one acylated kaempferol glycoside (pigment 9) were isolated from the blue flowers of cape stock (Heliophila coronopifolia) in Brassicaceae along with two known acylated cyanidin glycosides (pigments 7 and 8). Pigments 1-8, based on 3-sambubioside-5-glucosides of delphinidin and cyanidin, were acylated with hydroxycinnamic acids at 3-glycosyl residues of anthocyanidins. Using spectroscopic and chemical methods, the structures of pigments 1, 2, 5, and 6 were determined to be: delphinidin 3-O-[2-O-(β-xylopyranosyl)-6-O-(acyl)-β-glucopyranoside]-5-O-[6-O-(malonyl)-β-glucopyranoside], in which acyl moieties were, respectively, cis-p-coumaric acid for pigment 1, trans-caffeic acid for pigment 2, trans-p-coumaric acid for pigment 5 (a main pigment) and trans-ferulic acid for pigment 6, respectively. Moreover, the structure of pigments 3 and 4 were elucidated, respectively, as a demalonyl pigment 5 and a demalonyl pigment 6. Two known anthocyanins (pigments 7 and 8) were identified to be cyanidin 3-(6-p-coumaroyl-sambubioside)-5-(6-malonyl-glucoside) for pigment 7 and cyanidin 3-(6-feruloyl-sambubioside)-5-(6-malonyl-glucoside) for pigment 8 as minor anthocyanin pigments. A flavonol pigment (pigment 9) was isolated from its flowers and determined to be kaempferol 3-O-[6-O-(trans-feruloyl)-β-glucopyranoside]-7-O-cellobioside-4'-O-glucopyranoside as the main flavonol pigment. On the visible absorption spectral curve of the fresh blue petals of this plant and its petal pressed juice in the pH 5.0 buffer solution, three characteristic absorption maxima were observed at 546, 583 and 635 nm. However, the absorption curve of pigment 5 (a main anthocyanin in its flower) exhibited only one maximum at 569 nm in the pH 5.0 buffer solution, and violet color. The color of pigment 5 was observed to be very unstable in the pH 5.0 solution and soon decayed. In the pH 5.0 solution, the violet color of pigment 5 was restored as pure

  2. Synchrotron powder diffraction on Aztec blue pigments

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez del Rio, M. [European Synchrotron Radiation Facility, B.P. 220, Grenoble Cedex (France); Gutierrez-Leon, A.; Castro, G.R.; Rubio-Zuazo, J. [Spanish CRG Beamline at the European Synchrotron Radiation Facility, SpLine, B.P. 220, Grenoble Cedex (France); Solis, C. [Universidad Nacional Autonoma de Mexico, Instituto de Fisica, Mexico, D.F. (Mexico); Sanchez-Hernandez, R. [INAH Subdireccion de Laboratorios y Apoyo Academico, Mexico, D.F. (Mexico); Robles-Camacho, J. [INAH Centro Regional Michoacan, Morelia, Michoacan (Mexico); Rojas-Gaytan, J. [INAH Direccion de Salvamento Arqueologico, Naucalpan de Juarez (Mexico)

    2008-01-15

    Some samples of raw blue pigments coming from an archaeological rescue mission in downtown Mexico City have been characterized using different techniques. The samples, some recovered as a part of a ritual offering, could be assigned to the late Aztec period (XVth century). The striking characteristic of these samples is that they seem to be raw pigments prior to any use in artworks, and it was possible to collect a few {mu}g of pigment after manual grain selection under a microscopy monitoring. All pigments are made of indigo, an organic colorant locally known as anil or xiuhquilitl. The colorant is always found in combination with an inorganic matrix, studied by powder diffraction. In one case the mineral base is palygorskite, a rare clay mineral featuring micro-channels in its structure, well known as the main ingredient of the Maya blue pigment. However, other samples present the minerals sepiolite (a clay mineral of the palygorskite family) and calcite. Another sample contains barite, a mineral never reported in prehispanic paints. We present the results of characterization using high resolution powder diffraction recorded at the European Synchrotron Radiation Facility (BM25A, SpLine beamline) complemented with other techniques. All of them gave consistent results on the composition. A chemical test on resistance to acids was done, showing a high resistance for the palygorskite and eventually sepiolite compounds, in good agreement with the excellent resistance of the Maya blue. (orig.)

  3. Tailored surface engineering of pigments by layer-by-layer coating.

    Science.gov (United States)

    Dähne, Lars; Schneider, Julia; Lewe, Dirk; Petersen, Henrik

    2015-01-01

    We have evaluated the feasibility of layer-by-layer encapsulation technology for the improvement of dye pigments used for tattoos or permanent make-up. The formation of core-shell structures is possible by coating pigments with thin films of several different polyelectrolytes using this technology. The physicochemical surface properties, such as charge density and chemical functionality, can be reproducibly varied in a wide range. Tailoring the surface properties independently from the pigment core allows one to control the rheological behaviour of pigment suspensions, to prevent aggregation between different pigments, to reduce the cytotoxicity, and to influence the response of phagocytes in order to have similar or the same uptake and bioclearance for all pigments. These properties determine the durability and colour tone stability of tattoos and permanent make-up.

  4. Chemical structure and dynamics. Annual report 1994

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  5. Annual Report 1998: Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  6. Microstructural, structural and optical properties of nanoparticles of PbO-CrO3 pigment synthesized by a soft route

    Directory of Open Access Journals (Sweden)

    V. D. Araújo

    2015-03-01

    Full Text Available PbCrO4 and Pb2CrO5 particles were synthesized by the polymeric precursor method. Structural and microstructural properties of the particles were characterized by scanning electron microscopy with field emission gun, X-ray diffraction, and Raman spectroscopy techniques. The diffuse reflectance technique was employed to study the optical properties in the 400-700 nm range. The optical bandgap of the samples was obtained indirectly. Colorimetric coordinates L*, a*, b* were calculated for the pigment powders as a function of the heat treatment (400-700 ºC. The powders displayed colors ranging from green to red. X-ray diffraction patterns showed the presence of monoclinic PbCrO4 phase in green samples, while red powders had a monoclinic Pb2CrO5 phase structure. The Raman spectra of the PbCrO4 and Pb2CrO5 powders were in good agreement with those reported in the literature. The synthesized compounds can be used as green and red pigments with high thermal stability.

  7. Structure-function relationship of the plant photosynthetic pigment-protein complex LHCII studied with molecular spectroscopy techniques.

    Science.gov (United States)

    Gruszecki, Wieslaw I

    2013-01-01

    LHCII, the largest plant photosynthetic pigment-protein complex of photosystem II, is a most abundant membrane protein in living organisms and comprises approximately half of the pool of chlorophyll molecules in the biosphere. The principal role of this pigment-protein complex is to collect sunlight quanta and transfer electronic excitations toward the reaction centers, where the primary photosynthetic electric charge separation reactions take place. The LHCII protein, as a major protein component of the photosynthetic membranes, modulates also the structural and dynamic properties of the lipid phase of the membranes. According to the recent concepts, one of the physiological roles of LHCII is also a protection of the photosynthetic apparatus against oxidative damage caused by illumination with high intensity light. Detailed examination of all those physiological functions of LHCII, in relation to the complex structure, was possible owing to the application of several molecular spectroscopy techniques. Some examples of such studies are presented in this chapter. The examples of application of steady-state and time-resolved fluorescence spectroscopy, Fourier-transform infrared absorption spectroscopy, and resonance Raman scattering spectroscopy are presented and discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson; KWAUK

    2007-01-01

    Around the turn of the present century,scholars began to recognize chemical engineering as a com-plex system,and have been searching for a convenient point of entry for refreshing its knowledge base.From our study of the dynamic structures of dispersed particles in fluidization and the resultingmulti-scale method,we have been attempting to extend our findings to structures prevailing in othermultiphase systems as well as in the burgeoning industries producing functional materials.Chemicalengineering itself is hierarchically structured.Besides structures based on space and time,such hier-archy could be built from ChE history scaled according to science content,or from ChE operation ac-cording to the expenditure of manpower and capital investment.

  9. Structure of Pigment Yellow 181 dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate from XRPD plus DFT-D

    DEFF Research Database (Denmark)

    van de Streek, Jacco

    2015-01-01

    With only a 2.6 Å resolution laboratory powder diffraction pattern of the phase of Pigment Yellow 181 (P.Y. 181) available, crystal-structure solution and Rietveld refinement proved challenging; especially when the crystal structure was shown to be a triclinic dimethylsulfoxide N-methyl-2...

  10. Preparation and characterization of Cr203 system optically variable pigment

    Institute of Scientific and Technical Information of China (English)

    DU Haiyan; ZHANG Hua; CHEN Qirong; SUN Jiayue; XU Wencai; MA Erjun

    2007-01-01

    An optically variable pigment was produced by wet chemical method, where TiO2-coated mica with interfer-ence colors acted as the substrate materials. The structure of the pigment was characterized by X-ray diffraction (XRD),and its optically variable effect was investigated by X-Rite MA86 Ⅱ five angles spectrophotometer. The impact of differ-ent interference substrate materials for improving the color travel effect was studied, and the influence of white and black background on the hue and the color travel effect were stud-ied. Results showed that optically variable pigments can be prepared by coating Cr2O3 on the surface of the pretreated TiO2-coated mica. The color travel effect was sensitive to the change of substrate materials, and different backgrounds can influence the hue and the color travel effect of the pigment.

  11. Pigments Elementary Chemical Composition Study of a Gainsborough Attributed Painting Employing a Portable X-Rays Fluorescence System

    Science.gov (United States)

    Appoloni, C. R.; Blonski, M. S.; Parreira, P. S.; Souza, L. A. C.

    2007-02-01

    The investigated painting, identified with the title "The woodman", is attributed to Thomas Gainsborough (XVIII century) and is under investigation at the Laboratory of Conservation Science (LACICOR), CECOR/EBA/UFMG. The measurements were carried out with a portable X-rays fluorescence (XRF) system constituted of a X-rays tube with Ag anode, a Si PIN — diode detector, nuclear electronic chain and a special designed mechanical system for the detector and X-ray tube positioning, that enables angular and XYZ movements of the excitation-detection system. The employed voltage and current intensity were 17 kV and 3 mA, respectively. The time of acquisition for each measurement was 500 s. XRF spectra were analyzed using the AXIL-WinQXAS software. Three measurements in each of the following regions of the painting were done: face, leaves, arm, sky and firewood. The carried out analysis indicated the following pigments: White (lead white and calcium sulfate, identified by the elements Pb, Ca and S), Blue (Prussian blue, identified by the key element Fe), Red (Vermilion, identified by the elements Hg and S) and Brown (mixture of Fe and Mn oxides, identified by the elements Fe and Mn). Elements belonging to modern pigments corresponding to the same colors were absent in the analyzed spectra.

  12. The chemical bond structure and dynamics

    CERN Document Server

    Zewail, Ahmed

    1992-01-01

    This inspired book by some of the most influential scientists of our time--including six Nobel laureates--chronicles our emerging understanding of the chemical bond through the last nine decades and into the future. From Pauling's early structural work using x-ray and electron diffraction to Zewail's femtosecond lasers that probe molecular dynamics in real time; from Crick's molecular biology to Rich's molecular recognition, this book explores a rich tradition of scientific heritage and accomplishment. The perspectives given by Pauling, Perutz, Rich, Crick, Porter, Polanyi, Herschbach, Zewail,

  13. Síntese de pigmentos cerâmicos por precipitação química Synthesis of ceramic pigments by chemical precipitation

    Directory of Open Access Journals (Sweden)

    R. N. de Almeida

    2007-03-01

    Full Text Available Os pigmentos cerâmicos são substâncias capazes de desenvolver cor em sólido inorgânico (cerâmica ou vidro quando nele dispersar mantendo-se insolúvel no mesmo, sem reação química com o mesmo, nas elevadas temperaturas de processamento. Óxidos de cobre dão origem a pigmentos verdes que se decompõem em temperaturas relativamente baixas (em torno de 900 ºC enquanto adição de outros íons em sua composição poderá melhorar a sua estabilidade térmica e facilitar a sua utilização em revestimentos cerâmicos queimados em altas temperaturas. O presente trabalho teve por objetivo sintetizar, pelo método da precipitação (ou co-precipitação química, pós de óxidos de cobre e de manganês, tanto puros quanto misturados destinados ao uso em esmaltes decorativos de matriz vítrea. Para tal fim, pó de frita de vidro foi produzido pela fusão de feldspato do Seridó (divisa entre Paraíba e Rio Grande do Norte. Massas selecionadas, 5 a 10% em peso, de pigmentos foram misturadas com o referido pó de frita e a barbotina resultante foi aplicada sobre a superfície de placas de alumina densa, seguindo-se secagem e queima em escolhidas temperaturas. As cores dos recobrimentos obtidos foram avaliadas por medidas colorimétricas usando o sistema CIEL*a*b* e os resultados variaram em função da composição e teor de pigmentos, bem como da temperatura de queima. Constatou-se que os pigmentos de óxidos puros de cobre e de manganês deram tonalidades mais claras do que aquelas fornecidas pelo pigmento misto de cobre e de manganês.Ceramic pigments are substances that develop color in inorganic solids (ceramic or glass into which are capable of dispersing themselves at high processing temperatures without dissolution or chemical reaction. Copper oxides give rise to green pigments that undergo thermal decomposition at relatively low temperatures (about 900 ºC and the addition of other ions in its composition may improve its stability and

  14. Variability of phytoplankton absorption in the northern South China Sea: influence of the size structure and pigment composition of algal populations

    Institute of Scientific and Technical Information of China (English)

    WANG Guifen; CAO Wenxi; XU Dazhi; YANG Yuezhong

    2007-01-01

    Data from three cruises conducted in the Zhujiang River (ZR), coastal waters of Guangdong (CWGD) and the northern South China Sea (NSCS) during 2003 and 2004 were examined for assessing the relative importance of pigment composition and packaging effect in modifying the specific absorption coefficients of phytoplankton. The three survey regions differ widely in their phytoplankton community with large cells dominating the ZR and CWGD waters and small cells dominating the NSCS region. Variations in the size structure and the accessory pigments have much effect on the chlorophyll a-specific absorption coefficient of phytoplankton. The size index accounted for about 42% and 33% of the variation of the specific absorption coefficient at 440 and 675 nm, respectively. Using the multiple regression analysis approach, pigment concentrations for each sample were calculated. The accessory pigments other than chlorophyll a contribute to absorption mainly in the blue - to - green region of the spectrum and their absorptions account for about 44%, 43% and 53% on the average of the total phytoplankton absorption at 440 nm for the ZR, CWGD and NSCS regions. Among the accessory pigments, the photosynthetic carotenoids (noted PSC) play a dominant role in the ZR and CWGD waters, while in the NSCS the nonphotosynthetic carotenoids (noted PPG) as well as PSC have important contributions. Because the variations of both the size structure and accessory pigments in algal populations contributed to the variability of the specific absorption coefficient in the study regions, these factors may be considered explicitly in future bio - optical algorithms to derive chlorophyll a concentration more accurately.

  15. Trends in information theory-based chemical structure codification.

    Science.gov (United States)

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  16. Observations on phytoplankton pigments, zooplankton and physico-chemical parameters in surface waters from southern Indian Ocean and Antarctic region

    Digital Repository Service at National Institute of Oceanography (India)

    JiyalalRam, M.; Goswami, S.C.

    Observations on distribution of chlorophyll a, phaeopigments, zooplankton and physico-chemical parameters in the Southern Ocean were carried out during 9th Indian Antarctic-Expedition (1989-1990). The results indicated high phytoplankton biomass...

  17. Reaction centers of photosystem II with a chemically-modified pigment composition: exchange of pheophytins with 13(1)-deoxo-13(1)-hydroxy-pheophytin a.

    Science.gov (United States)

    Shkuropatov AYa; Khatypov, R A; Shkuropatova, V A; Zvereva, M G; Owens, T G; Shuvalov, V A

    1999-04-30

    Isolated reaction centers of photosystem II with an altered pigment content were obtained by chemical exchange of the native pheophytin a molecules with externally added 13(1)-deoxo-13(1)-hydroxy-pheophytin a. Judged from a comparison of the absorption spectra and photochemical activities of exchanged and control reaction centers, 70-80% of the pheophytin molecules active in charge separation are replaced by 13(1)-deoxo-13(1)-hydroxy-pheophytin a after double application of the exchange procedure. The new molecule at the active branch was not active photochemically. This appears to be the first stable preparation in which a redox active chromophore of the reaction center of photosystem II was modified by chemical substitution. The data are compatible with the presence of an active and inactive branch of cofactors, as in bacterial reaction centers. Possible applications of the 13(1)-deoxo-13(1)-hydroxy-pheophytin a-exchanged preparation to the spectral and functional analysis of native reaction centers of photosystem II are discussed.

  18. Structures and Stabilization Mechanisms in Chemically Stabilized Ceramics

    Science.gov (United States)

    Gai-Boyes, Pratibha L.; Saltzberg, Michael A.; Vega, Alexander

    1993-09-01

    Structural complexities and disorder in chemically stabilized cristobalites (CSC), which are room temperature silica-based ceramics, prepared by a wet chemical route, are described. CSC displays many of the structural characteristics of the high temperature cristobalite, elucidated by HREM and X-ray diffraction. In-situ electron diffraction and NMR results suggest that the disorder is structural and is static.

  19. Chemical and Mechanical Weed Control Methods and Their Effects on Photosynthetic Pigments and Grain Yield of Kidney Bean

    Directory of Open Access Journals (Sweden)

    A.S Ghatari

    2015-11-01

    Full Text Available To evaluate the integrated management of weeds in red kidney bean, a split-plot experiment using randomized complete block design with three replications was conducted in 2013 in the Damavand County. In this experiment, the mechanical control treatments consisted of two levels (no cultivation and one cultivation asseigned to main plots and controlling chemical treatments consisted of six levels (non-application of herbicides, pre-emergence herbicide application of Pursuit with full dose of 1 liter per hectare, pre-emergence herbicide application of Pursuit a dose decreased 0.5 liters per hectare, post-emergence herbicide application of Pursuit dose reduced to 0.3 liters per hectare + 2 thousand citogate, post-emergence herbicide application of Pursuit with a reduced dose of 0.5 liters per hectare + 2 thousand citogate, post-emergence herbicide application of Pursuit full dose of 1 liter per hectar + 2 thousand citogate to subplots. The results showed that the effects of interaction between herbicide application and cultivation for traits of carotenoids, chlorophyll a, chlorophyll b and total chlorophyll contents, density of weeds and their dry weights were significant at 1 %, and grain yield at the 5% probability levels. The highest bean seed yield with an average of 5461.6 kg.ha-1 and lowest weed dry weight with an average of 345.9 kg.ha-1 were related to pre-emergence herbicide and cultivation with a dose of 1 liter per hectare treatment. The difference between full and reduced doses of chemical weed control was non-significant. It could be concluded that integrated mechanical and chemical weed control not only may increase seed yield but also reduce, environmental hazards.

  20. Fine structure of the retinal pigment epithelium in the Port Jackson shark (Heterodontus phillipi).

    Science.gov (United States)

    Braekevelt, C R

    1994-11-01

    The structure of the retinal epithelium (RPE), choriocapillaris and Bruch's membrane (complexus basalis) has been studied by light and electron microscopy in the Port Jackson shark (Heterodontus phillipi). In this elasmobranch the RPE consists of a single layer of low cuboidal cells which show basal (scleral) infolding and apical (vitreal) processes that enclose photoreceptor outer segments. Laterally these epithelial cells are joined by a series of apically located tight junctions. The RPE cells display a large vesicular nucleus, abundant smooth endoplasmic reticulum as well as numerous polysomes and mitochondria. Phagosomes are present, rough endoplasmic reticulum is scarce and myeloid bodies were not observed. Melanosomes are absent over the choroidally located tapetum lucidum, but are not abundant even in extratapetal areas. This paucity of melanosomes probably makes retinomotor movements unimportant. Bruch's membrane or complexus basalis is a pentalaminate structure. The endothelium of the choriocapillaris is thin but minimally fenestrated.

  1. Physical and chemical property of Guangxi Zhuang Medicine Coix lachryma-jobi L.stem pigment%广西壮药薏苡茎色素的理化性质研究

    Institute of Scientific and Technical Information of China (English)

    余珊; 梁俏; 尤萍; 黄秀丽; 李雄; 黄锁义

    2012-01-01

    To stem the material Guangxi Zhuang Medicine Coix lachryma-jobi L., Study on the Coix lachryma-jobi L. Stem pigment of physical and chemical property, to provide important new material for all kinds of new pigment used in food products,cosmetic and leeclidom etc. Coix lachryma-jobi L. Stem pigment extracted optimum conditions: water as extraction agent, room temperature, boiled 2h. Solid to liquid ratio of 1:50 (g/ml). UV analysis of stability of the pigment results show that: Pigment at 330nm maximum absorption peak, good water-soluble pigment, pH, a greater impact on the stability of the pigment, but the good thermal stability. Preservatives and starch on the stability of the pigment no adverse effect, light is poor. Oxidants, reducing agents, in addition to significant effect of ascorbic acid on the pigment, the other had no significant effect. In addition to Fe3+, the metal ions on the less affected.%以广西壮药薏苡茎为材料,对薏苡茎色素的理化性质进行研究,为生产各种食用品、化妆品、医药药品等色素新产品提供重要原料.提取薏苡茎色素的最佳工艺条件为:以水作提取剂,室温下煮沸2h,料液比为1∶50 (g/mL).用紫外分析法研究色素稳定性.结果表明:色素在330nm处有最大吸收峰,色素水溶性较好,pH值对色素的稳定性影响较大,但热稳定性良好.防腐剂、淀粉对色素的稳定性无不良影响,耐光性较差.氧化剂、还原剂中除抗坏血酸对色素的影响明显外,其他均无明显影响.除Fe3+外,金属离子对其影响较小.

  2. Retinal pigment epithelial fine structure in the red-tailed hawk (Buto jamaicensis).

    Science.gov (United States)

    Braekevelt, C R

    1992-03-01

    As part of a comparative morphological study, the fine structure of the retinal epithelium (RPE), choriocapillaris and Bruch's membrane (complexus basalis) has been studied by electron microscopy in the red-tailed hawk (Buteo jamaicensis). In this species the RPE consists of a single layer of low cuboidal cells which display numerous basal (scleral) infoldings and extensive apical (vitreal) processes which interdigitate with photoreceptor outer segments. These epithelial cells are joined laterally by a series of basally located tight junctions. Internally SER is the most abundant cell organelle while only small amounts of RER are present. Polysomes are however abundant as are mitochondria. The RPE cell nucleus is large and vesicular. Melanosomes are mainly located in the apical processes of the RPE cells in light-adaptation. Myeloid bodies are large and numerous in light-adaptation and often show ribosomes on their outer border. Bruch's membrane (complexus basalis) shows the typical pentalaminate structure noted in most vertebrates but with only a poorly defined central elastic layer. The endothelium of the choriocapillaris is very thin facing the RPE but is only moderately fenestrated. The choriocapillaris in this species is unusual however in that many of the fenestrae show a double-layered diaphragm.

  3. Skin Pigmentation Disorders

    Science.gov (United States)

    Pigmentation means coloring. Skin pigmentation disorders affect the color of your skin. Your skin gets its color from a pigment called melanin. Special cells in the skin make melanin. When these cells become damaged or ...

  4. Structure and barrier properties of human embryonic stem cell-derived retinal pigment epithelial cells are affected by extracellular matrix protein coating.

    Science.gov (United States)

    Sorkio, Anni; Hongisto, Heidi; Kaarniranta, Kai; Uusitalo, Hannu; Juuti-Uusitalo, Kati; Skottman, Heli

    2014-02-01

    Extracellular matrix (ECM) interactions play a vital role in cell morphology, migration, proliferation, and differentiation of cells. We investigated the role of ECM proteins on the structure and function of human embryonic stem cell-derived retinal pigment epithelial (hESC-RPE) cells during their differentiation and maturation from hESCs into RPE cells in adherent differentiation cultures on several human ECM proteins found in native human Bruch's membrane, namely, collagen I, collagen IV, laminin, fibronectin, and vitronectin, as well as on commercial substrates of xeno-free CELLstart™ and Matrigel™. Cell pigmentation, expression of RPE-specific proteins, fine structure, as well as the production of basal lamina by hESC-RPE on different protein coatings were evaluated after 140 days of differentiation. The integrity of hESC-RPE epithelium and barrier properties on different coatings were investigated by measuring transepithelial resistance. All coatings supported the differentiation of hESC-RPE cells as demonstrated by early onset of cell pigmentation and further maturation to RPE monolayers after enrichment. Mature RPE phenotype was verified by RPE-specific gene and protein expression, correct epithelial polarization, and phagocytic activity. Significant differences were found in the degree of RPE cell pigmentation and tightness of epithelial barrier between different coatings. Further, the thickness of self-assembled basal lamina and secretion of the key ECM proteins found in the basement membrane of the native RPE varied between hESC-RPE cultured on compared protein coatings. In conclusion, this study shows that the cell culture substrate has a major effect on the structure and basal lamina production during the differentiation and maturation of hESC-RPE potentially influencing the success of cell integrations and survival after cell transplantation.

  5. Determination of the structure of the violet pigment C22H12Cl2N6O4 from a non-indexed X-ray powder diagram.

    Science.gov (United States)

    Schmidt, Martin U; Ermrich, Martin; Dinnebier, Robert E

    2005-02-01

    The violet pigment methylbenzimidazolonodioxazine, C22H12Cl2N6O4 (systematic name: 6,14-dichloro-3,11-dimethyl-1,3,9,11-tetrahydro-5,13-dioxa-7,15-diazadiimidazo-[4,5-b:4',5'-m]pentacene-2,10-dione), shows an X-ray powder diagram consisting of only ca 12 broad peaks. Indexing was not possible. The structure was solved by global lattice energy minimizations. The program CRYSCA [Schmidt & Kalkhof (1999), CRYSCA. Clariant GmbH, Pigments Research, Frankfurt am Main, Germany] was used to predict the possible crystal structures in different space groups. By comparing simulated and experimental powder diagrams, the correct structure was identified among the predicted structures. Owing to the low quality of the experimental powder diagram the Rietveld refinements gave no distinctive results and it was difficult to prove the correctness of the crystal structure. Finally, the structure was confirmed to be correct by refining the crystal structure of an isostructural mixed crystal having a better X-ray powder diagram. The compound crystallizes in P1, Z=1. The crystal structure consists of a very dense packing of molecules, which are connected by hydrogen bridges of the type N-H...O=C. This packing explains the observed insolubility. The work shows that crystal structures of molecular compounds may be solved by lattice energy minimization from diffraction data of limited quality, even when indexing is not possible.

  6. ACToR Chemical Structure processing using Open Source ...

    Science.gov (United States)

    ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

  7. How to add chemical abstracts service registry numbers and structures to databases via chemical names comparison

    Science.gov (United States)

    Krebs; Jordis

    2000-03-01

    For the conversion of nonstructural chemical databases to structure databases, a series of algorithms to find the closest match between existing names to names in a reference database are described. On the basis of the best match, new fields such as the Chemical Abstracts Service Registry Number (CASRN) or structures were added to the database.

  8. Thin Layer Chromatography (TLC) of Chlorophyll Pigments.

    Science.gov (United States)

    Foote, Jerry

    1984-01-01

    Background information, list of materials needed, procedures used, and discussion of typical results are provided for an experiment on the thin layer chromatography of chlorophyll pigments. The experiment works well in high school, since the chemicals used are the same as those used in paper chromatography of plant pigments. (JN)

  9. Thin Layer Chromatography (TLC) of Chlorophyll Pigments.

    Science.gov (United States)

    Foote, Jerry

    1984-01-01

    Background information, list of materials needed, procedures used, and discussion of typical results are provided for an experiment on the thin layer chromatography of chlorophyll pigments. The experiment works well in high school, since the chemicals used are the same as those used in paper chromatography of plant pigments. (JN)

  10. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  11. Mapping chemical performance on molecular structures using locally interpretable explanations

    CERN Document Server

    Whitmore, Leanne S; Hudson, Corey M

    2016-01-01

    In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. This method of "painting" locally interpretable explanations onto 2-D chemical structures replicates the chemical intuition of synthetic chemists, allowing researchers in the field to directly accept, reject, inform and evaluate decisions underlying inscrutably complex quantitative structure-activity relationship models.

  12. SOME QUANTUM CHEMICAL STUDY ON THE STRUCTURAL ...

    African Journals Online (AJOL)

    Preferred Customer

    Formula. Formula weight. (gmol-1) ... Quantum chemical calculations (Density Functional Theory, B3LYP/6-31G (d)) were used to purposed the ... correlation functional [B3LYP/6-31G(d)]) calculations were done by using Gaussian 03 program ...

  13. Molecular and structural characterization of some violet phosphate pigments for their non-invasive identification in modern paintings

    Science.gov (United States)

    Anselmi, C.; Vagnini, M.; Cartechini, L.; Grazia, C.; Vivani, R.; Romani, A.; Rosi, F.; Sgamellotti, A.; Miliani, C.

    2017-02-01

    A complete non-invasive characterization by XRF, XRD, near-FTIR and UV-Vis reflectance spectroscopy has been performed on some commercially available violet pigments as well as on pure violet Co-salts also known to be used as pigments. The obtained results show that, after a preliminary elemental characterization, the studied pigments can be easily identified by near-FTIR and UV-Vis spectroscopies since they exhibit peculiar spectral bands in these regions. Among the analyzed samples emerged that the pigment 45350 - "Manganviolett" from Kremer consists of two α- and β-NH4MnP2O7 polymorphs, being α-NH4MnP2O7 the most abundant one; furthermore we found that the pigment R1215D -"Cobalt violet" by Winsor & Newton (no longer available since 2006) displays spectral features that match exactly those of 45820-"Kobaltviolett hell" from Kremer and both are composed by cobalt ammonium phosphate hydrate. Such non-invasive study allowed for the identification of "Manganese Violet" (α-NH4MnP2O7) and anhydrous cobalt phosphate (Co3(PO4)2) on some Boccioni's paintings during MOLAB in situ measurements at the Museo del Novecento (Milano). The spectrum of sample 6 shows, as expected, the O-P-O bending and P-O stretching vibrational multiple bands in the ranges of 420-700 cm-1 and 1000-1250 cm-1, while the peaks located at 760 and 912 cm-1 are attributed to the symmetric and antisymmetric P-O-P vibrations that are typical of the pyrophosphate group. [4]. Characteristic stretching and bending absorptions of the NH4+ cation are visible in the range 3300-3000 cm-1, and at about 1450-1400 cm-1. Typical spectral features of kaolin are visible at 3620 and 3694 cm-1[5].

  14. Cribrarione C, a naphthoquinone pigment from the myxomycete Cribraria meylanii.

    Science.gov (United States)

    Shintani, Akinori; Yamazaki, Hiroyuki; Yamamoto, Yukinori; Ahmed, Firoj; Ishibashi, Masami

    2009-08-01

    Chemical investigation of field-collected fruit bodies of the myxomycete Cribraria meylanii resulted in the isolation of a naphthoquinone pigment, cribrarione C, and its structure was elucidated by spectral data as 2,5,6,7-tetrahydroxy-1,4-naphthoquinone (1). This compound (1) had been synthesized previously, while it was isolated here for the first time as a natural product, and its NMR and MS data are described in this study.

  15. A genomic and transcriptomic approach to investigate the blue pigment phenotype in Pseudomonas fluorescens.

    Science.gov (United States)

    Andreani, Nadia Andrea; Carraro, Lisa; Martino, Maria Elena; Fondi, Marco; Fasolato, Luca; Miotto, Giovanni; Magro, Massimiliano; Vianello, Fabio; Cardazzo, Barbara

    2015-11-20

    Pseudomonas fluorescens is a well-known food spoiler, able to cause serious economic losses in the food industry due to its ability to produce many extracellular, and often thermostable, compounds. The most outstanding spoilage events involving P. fluorescens were blue discoloration of several food stuffs, mainly dairy products. The bacteria involved in such high-profile cases have been identified as belonging to a clearly distinct phylogenetic cluster of the P. fluorescens group. Although the blue pigment has recently been investigated in several studies, the biosynthetic pathway leading to the pigment formation, as well as its chemical nature, remain challenging and unsolved points. In the present paper, genomic and transcriptomic data of 4 P. fluorescens strains (2 blue-pigmenting strains and 2 non-pigmenting strains) were analyzed to evaluate the presence and the expression of blue strain-specific genes. In particular, the pangenome analysis showed the presence in the blue-pigmenting strains of two copies of genes involved in the tryptophan biosynthesis pathway (including trpABCDF). The global expression profiling of blue-pigmenting strains versus non-pigmenting strains showed a general up-regulation of genes involved in iron uptake and a down-regulation of genes involved in primary metabolism. Chromogenic reaction of the blue-pigmenting bacterial cells with Kovac's reagent indicated an indole-derivative as the precursor of the blue pigment. Finally, solubility tests and MALDI-TOF mass spectrometry analysis of the isolated pigment suggested that its molecular structure is very probably a hydrophobic indigo analog.

  16. Marine chemical ecology: chemical signals and cues structure marine populations, communities, and ecosystems.

    Science.gov (United States)

    Hay, Mark E

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  17. Pigments, patterns, and fish behavior.

    Science.gov (United States)

    Price, Anna C; Weadick, Cameron J; Shim, Janet; Rodd, F Helen

    2008-12-01

    Color patterns in fish are often multicomponent signals, composed of pigment-based and structural color patches that can be used to communicate within species, in both inter- and intrasexual interactions, and between species. In this review, we discuss some of the roles played by pigment-based elements of color pattern. We begin by discussing general forms of coloration, classifying them by appearance (e.g., cryptic vs. conspicuous) and apparent function (e.g., conspicuous coloration and mating displays, stripes and cooperation, and bars and aggression). We then briefly discuss the roles pigments play in the perception of these color patterns via their presence in the eye. In the last section, we look at the relative importance of carotenoid versus melanic coloration in situations where honest signals to potential rivals and potential mates might be required. In this survey, we have highlighted some recent research, especially studies that consider both the physiological and behavioral processes underlying the evolution and expression of pigment-based color patterns in fish. The nature of pigmented color patterns depends not just on the dynamics of pattern development and physiological regulation, but also on the behavioral roles played by these patterns, both now and in the past. As such, advances in particular fields of study on pigment patterns (physiology, developmental biology, behavioral ecology, evolutionary biology, etc.) will increasingly depend on insights from other fields.

  18. Bayesian inference of protein structure from chemical shift data

    Science.gov (United States)

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  19. Estimation of molar absorptivities and pigment sizes for eumelanin and pheomelanin using femtosecond transient absorption spectroscopy

    Science.gov (United States)

    Piletic, Ivan R.; Matthews, Thomas E.; Warren, Warren S.

    2009-11-01

    Fundamental optical and structural properties of melanins are not well understood due to their poor solubility characteristics and the chemical disorder present during biomolecular synthesis. We apply nonlinear transient absorption spectroscopy to quantify molar absorptivities for eumelanin and pheomelanin and thereby get an estimate for their average pigment sizes. We determine that pheomelanin exhibits a larger molar absorptivity at near IR wavelengths (750nm), which may be extended to shorter wavelengths. Using the molar absorptivities, we estimate that melanin pigments contain ˜46 and 28 monomer units for eumelanin and pheomelanin, respectively. This is considerably larger than the oligomeric species that have been recently proposed to account for the absorption spectrum of eumelanin and illustrates that larger pigments comprise a significant fraction of the pigment distribution.

  20. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim

    2015-01-01

    content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain......, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however......Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...

  1. Nematic films at chemically structured surfaces

    Science.gov (United States)

    Silvestre, N. M.; Telo da Gama, M. M.; Tasinkevych, M.

    2017-02-01

    We investigate theoretically the morphology of a thin nematic film adsorbed at flat substrate patterned by stripes with alternating aligning properties, normal and tangential respectively. We construct a simple ‘exactly-solvable’ effective interfacial model where the liquid crystal distortions are accounted for via an effective interface potential. We find that chemically patterned substrates can strongly deform the nematic-air interface. The amplitude of this substrate-induced undulations increases with decreasing average film thickness and with increasing surface pattern pitch. We find a regime where the interfacial deformation may be described in terms of a material-independent universal scaling function. Surprisingly, the predictions of the effective interfacial model agree semi-quantitatively with the results of the numerical solution of a full model based on the Landau-de Gennes theory coupled to a square-gradient phase field free energy functional for a two phase system.

  2. Research on the Structure of Grape Pigment%葡萄色素结构的研究

    Institute of Scientific and Technical Information of China (English)

    王颖; 吴冬

    2012-01-01

    This experiment has preliminarily identified the the pigment extracted from the grape peel, using the skin of grapes as raw materials. The result of this study showed that the pigment from the skin of grapes is a kind of flavonoid compounds with phenol hydroxyl, which contained glucoside. The research provided reliably theoretical basis for the development and utilization of the grape skin pigment in food and pharmaceutical industries.%本实验以葡萄皮为原料.对葡萄皮的色素结构进行了初步鉴定,其研究结果表明:葡萄皮色素是一种带有酚羟基的黄酮类化合物,其中含有葡萄糖苷。通过实验研究为葡萄皮色素在食品、医药工业中的开发、利用提供了可靠的理论依据。

  3. Characteristics of Phytoplankton Community Structure During and After a Bloom of the Dinoflagellate Scrippsiella trochoidea by HPLC Pigment Analysis

    Institute of Scientific and Technical Information of China (English)

    WONG Chun-kwan; WONG Chong-kim

    2009-01-01

    A bloom of the dinoflagellate Scrippsiella trochoidea was detected for the first time in inner Tolo Harbor, Hong Kong in 2000. Water samples were collected at eight stations along a transect passing through a red tide patch for microscopic analysis of phytoplankton composition and high-performance liquid chromatography (HPLC) analysis of phytoplankton pigments. During the bloom, the density of dinoflagellates was 1.1×106 cells L-1 within the patch and 8.6×105 cells L-1 outside the patch where the phyto-plankton community was dominated by diatoms. After the bloom the S. trochoidea began to decrease in density and was replaced by diatoms as the dominating bloom-causing organisms at all stations, and the density of dinoflagellates at most stations was less than 1.0×106 cells L-1. The status of S. trochoidea as the causative species of the bloom was indicated by the presence of peridinin, the marker pigment for dinoflagellates. The shift from dinoflagellates to diatoms was marked by the decline of peridinin and the preva-lence of fucoxanthin. Phytoplankton pigment markers also revealed the presence of other minor phytoplankton assemblages such as cryptomonads and blue-green algal.

  4. Marennine, Promising Blue Pigments from a Widespread Haslea Diatom Species Complex

    Directory of Open Access Journals (Sweden)

    Romain Gastineau

    2014-05-01

    Full Text Available In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

  5. Marennine, promising blue pigments from a widespread Haslea diatom species complex.

    Science.gov (United States)

    Gastineau, Romain; Turcotte, François; Pouvreau, Jean-Bernard; Morançais, Michèle; Fleurence, Joël; Windarto, Eko; Prasetiya, Fiddy Semba; Arsad, Sulastri; Jaouen, Pascal; Babin, Mathieu; Coiffard, Laurence; Couteau, Céline; Bardeau, Jean-François; Jacquette, Boris; Leignel, Vincent; Hardivillier, Yann; Marcotte, Isabelle; Bourgougnon, Nathalie; Tremblay, Réjean; Deschênes, Jean-Sébastien; Badawy, Hope; Pasetto, Pamela; Davidovich, Nikolai; Hansen, Gert; Dittmer, Jens; Mouget, Jean-Luc

    2014-05-28

    In diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. The marine pennate diatom Haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. This pigment, responsible for the greening of oysters in western France, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. A method to extract and purify marennine has been developed, but its chemical structure could hitherto not be resolved. For decades, H. ostrearia was the only organism known to produce marennine, and can be found worldwide. Our knowledge about H. ostrearia-like diatom biodiversity has recently been extended with the discovery of several new species of blue diatoms, the recently described H. karadagensis, H. silbo sp. inedit. and H. provincialis sp. inedit. These blue diatoms produce different marennine-like pigments, which belong to the same chemical family and present similar biological activities. Aside from being a potential source of natural blue pigments, H. ostrearia-like diatoms thus present a commercial potential for aquaculture, cosmetics, food and health industries.

  6. Chemical isomeric effects on propanol glassy structures

    CERN Document Server

    Cuello, G J; Bermejo, F J; Cabrillo, C

    2002-01-01

    We have studied the structure of both propanol isomers in their glassy and crystalline states by neutron diffraction. The glass-transition temperatures of 1- and 2-propanol are about 98 and 115 K, respectively and, surprisingly, even larger differences are observed for the melting temperatures of the stable crystals, which are 148 and 185 K, respectively. Their supercooled liquid phases show rather different relaxation spectra, 1-propanol manifesting strong deviations from Debye behavior, whereas 2-propanol shows a far weaker effect. We discuss the spectra obtained for the static structure factor and the static pair correlation function D(r). There is a noticeable difference in the position of the first sharp diffraction peak, which clearly indicates a density change, well correlated with the period of the intermolecular oscillations shown by D(r). (orig.)

  7. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  8. Effect of different raw material color on physical and chemical properties of sorghum red pigment%不同原料颜色对高粱红色素理化性质的影响

    Institute of Scientific and Technical Information of China (English)

    李传欣; 张宏宇; 李景林

    2012-01-01

    分别采用红色和黑色两种颜色高粱壳为原料提取高粱红色素,对其理化性质分析比较,可知黑壳色素提取率为5.2%,色价45,耐热性能好,色调为紫褐色,色泽较暗;红壳色素提取率为3.1%,色价32,色调为红棕色,色泽较亮。%Sorghum red pigment extracted from red and black properties result was that the pigment extraction rate of black resistance was good,hue was purple and brown,color and lustre was 3.1%, color value was 32, hue was reddish brown, colour and color sorghum shell,physical and chemical shell was 5.2% ,color value was 45,heat was dark. Pigment extraction rate of red shell lustre was more bright.

  9. Structural and Chemical Diversity of Tl-Based Cuprate Superconductors

    Institute of Scientific and Technical Information of China (English)

    信赢

    2003-01-01

    The Tl-based cuprate superconductor family is the largest family in crystal structure and chemical composition among all high Tc cuprate superconductors. The Tl family can be divided into two sub-families, the Tl single layer family and the Tl double layer family, based on their crystal structural characteristics. The Tl single layer family is an ideal material for investigating the evolution of crystalline formation, charge carrier density, chemical composition, transport properties, superconductivity and their relationships. The Tl family contains almostall possible crystal structures discovered in high-Tc cuprate superconductors. Tl cuprate superconductors are of great importance not only in studying high-temperature superconductivity but also in commercial applications.

  10. Forgotten topological index of chemical structure in drugs.

    Science.gov (United States)

    Gao, Wei; Siddiqui, Muhammad Kamran; Imran, Muhammad; Jamil, Muhammad Kamran; Farahani, Mohammad Reza

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs.

  11. Classification of fossil fuels according to structural-chemical characteristics

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Gyul' maliev; G.S. Golovin; S.G. Gagarin [Institute for Fossil Fuels, Moscow (Russian Federation)

    2007-10-15

    On the basis of a set of linear equations that relate the amount of major elements n{sub E} (E = C, H, O, N, S) in the organic matter of fossil fuels to structural characteristics, such as the number of cycles R, the number of atoms n{sub E}, the number of mutual chemical bonds, the degree of unsaturation of the structure {delta}, and the extent of its reduction B, a structural-chemical classification of fossil coals that is closely related to the parameters of the industrial-genetic classification (GOST 25543-88) is proposed. Structural-chemical classification diagrams are constructed for power-generating coals of Russia; coking coals; and coals designed for nonfuel purposes including the manufacture of adsorbents, synthetic liquid fuel, ion exchangers, thermal graphite, and carbon-graphite materials.

  12. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  13. Pigmented Villonodular Synovitis (PVNS)

    Science.gov (United States)

    ... OverviewWhat is pigmented villonodular synovitis?Pigmented villonodular synovitis (PVNS) is a joint problem that usually affects the ... ankle, elbow, hand or foot.When you have PVNS, the lining of a joint becomes swollen and ...

  14. Oral pigmentation: A review.

    Science.gov (United States)

    Sreeja, C; Ramakrishnan, K; Vijayalakshmi, D; Devi, M; Aesha, I; Vijayabanu, B

    2015-08-01

    Pigmentations are commonly found in the mouth. They represent in various clinical patterns that can range from just physiologic changes to oral manifestations of systemic diseases and malignancies. Color changes in the oral mucosa can be attributed to the deposition of either endogenous or exogenous pigments as a result of various mucosal diseases. The various pigmentations can be in the form of blue/purple vascular lesions, brown melanotic lesions, brown heme-associated lesions, gray/black pigmentations.

  15. Visually Guiding and Controlling the Search While Mining Chemical Structures

    OpenAIRE

    Max Pereira; Vitor Santos Costa; Rui Camacho; Fonseca, Nuno A.

    2009-01-01

    In this paper we present the work in progress on LogCHEM, an ILP based tool for discriminative interactive mining of chemical fragments. In particular, we describe the integration with a molecule visualisation software that allows the chemist to graphically control the search for interesting patterns in chemical fragments. Furthermore, we show how structured information, such as rings, functional groups like carboxyl, amine, methyl, ester, etc are integrated and exploited in LogCHEM.

  16. Neovascularisation by tattoo pigment

    Directory of Open Access Journals (Sweden)

    Abdul Razack E

    1991-01-01

    Full Text Available Split skin grafting for the removal of a tattoo resulted in the appearance of pigmented papules in the periphery of the grafted skin as well as distal to it on the normal skin. Histologically they showed large vascular laminae containing red blood corpuscles and pigment deposits, a hitherto not documented complication of tattoo pigment.

  17. Overview of plant pigments

    Science.gov (United States)

    Chlorophylls, carotenoids, flavonoids and betalains are four major classes of biological pigments produced in plants. Chlorophylls are the primary pigments responsible for plant green and photosynthesis. The other three are accessary pigments and secondary metabolites that yield non-green colors and...

  18. Mining chemical structural information from the drug literature.

    Science.gov (United States)

    Banville, Debra L

    2006-01-01

    It is easier to find too many documents on a life science topic than to find the right information inside these documents. With the application of text data mining to biological documents, it is no surprise that researchers are starting to look at applications that mine out chemical information. The mining of chemical entities--names and structures--brings with it some unique challenges, which commercial and academic efforts are beginning to address. Ultimately, life science text data mining applications need to focus on the marriage of biological and chemical information.

  19. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  20. Physical and chemical properties of pigmented oil obtained from shrimp heads; Evaluacion fisico-quimica de aceite pigmentado obtenido de la cabeza de camaron

    Energy Technology Data Exchange (ETDEWEB)

    Nunez-Gastelum, J. A.; Sanchez-Machado, D. I.; Lopez-Cervantes, J.; Paseiro-Losada, P.; Sendon, R.; Sanchez-Silva, A. T.; Costa, H. S.; Aurrekoetxea, G. P.; Angulo, I.; Soto-Valdez, H.

    2011-07-01

    In this work the proximal analysis, physicochemical characterization, fatty acid profile and astaxanthin content of pigmented oil obtained by fermentation shrimp heads are presented. Lipids are the major components in the oil (95%). The saponification number is 178.62 mg KOH/g, iodine value 139.8 cg iodine/g, and the peroxide value was not detected. Density and viscosity were 0.92 mg/ml and 64 centipoises, respectively. The highest contents of fatty acids were linoleic (C18:2n6), oleic (C18:1n9) and palmitic (C16:0). Eicosapentaenoic acid (C20:5n3, EPA) and docosahexaenoic acid (C22:6n3, DHA) account for 9% of the total. The content of astaxanthin was 2.72 mg/g dry weight. The pigmented oil is a dietary source of nutrients with high value such as astaxanthin. (Author) 45 refs.

  1. The electronic structure and chemical bonding of vitamin B12

    Science.gov (United States)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  2. Understanding of the importance of the spore coat structure and pigmentation in the Bacillus subtilis spore resistance to low-pressure plasma sterilization

    Science.gov (United States)

    Raguse, Marina; Fiebrandt, Marcel; Denis, Benjamin; Stapelmann, Katharina; Eichenberger, Patrick; Driks, Adam; Eaton, Peter; Awakowicz, Peter; Moeller, Ralf

    2016-07-01

    Low-pressure plasmas have been evaluated for their potential in biomedical and defense purposes. The sterilizing effect of plasma can be attributed to several active agents, including (V)UV radiation, charged particles, radical species, neutral and excited atoms and molecules, and the electric field. Spores of Bacillus subtilis were used as a bioindicator and a genetic model system to study the sporicidal effects of low-pressure plasma decontamination. Wild-type spores, spores lacking the major protective coat layers (inner, outer, and crust), pigmentation-deficient spores or spore impaired in encasement (a late step in coat assembly) were systematically tested for their resistance to low-pressure argon, hydrogen, and oxygen plasmas with and without admixtures. We demonstrate that low-pressure plasma discharges of argon and oxygen discharges cause significant physical damage to spore surface structures as visualized by atomic force microscopy. Spore resistance to low-pressure plasma was primarily dependent on the presence of the inner, and outer spore coat layers as well as spore encasement, with minor or less importance of the crust and spore pigmentation, whereas spore inactivation itself was strongly influenced by the gas composition and operational settings.

  3. 黄姜色素理化性质的研究%Research on the Physical and Chemical Properties of Yellow Pigment from Dioscorea zingiberensis

    Institute of Scientific and Technical Information of China (English)

    舒国伟; 张倩; 陈合; 李世玉; 汪卓

    2015-01-01

    研究了大孔树脂纯化后的黄姜色素的颜色反应、溶解性以及pH、温度、光照、金属离子、氧化剂和还原剂对该色素稳定性的影响。结果表明:黄姜色素具有黄酮类的颜色反应特性,其易溶于甲醇、乙酸、乙醇和水,微溶于正丁醇,不溶于乙醚、乙酸乙酯和石油醚等脂溶性溶剂;其对碱性环境比较稳定,酸性环境变化较大,50℃以下较稳定,高温易变质,对自然光和紫外光稳定;Fe2+,Cu2+,Al3+,Na+,Mg2+, Zn2+,Ca2+,Mn2+等8种金属离子及还原剂Na2 SO3均导致黄姜色素溶液吸光度下降,氧化剂 H2 O2对黄姜色素有一定的增色作用。%The color reaction and solubility of yellow pigment from Dioscorea zingiberensis purified by macroporous resin XDA-7 and the effect of pH,temperature,light,metal ions,oxidizing and reducing agents on the stability of the pigment are studied.The results show that the yellow pigment is soluble in methanol,acetic acid,ethanol and water,slightly soluble in n-butanol,insoluble in ether,ethyl acetate and petroleum ether and other lipid-soluble solvent,which has color reaction characteristic of flavonoids;it is relatively stable in alkaline environment and has a significant change in the acidic environment;it is stable below 50 ℃ or under natural light and UV and changes in high temperature;8 kinds of metal ions including Fe2+,Cu2+,Al3+,Na+,Mg2+,Zn2+,Ca2+ and Mn2+and reducing agent Na2 SO3 all lead to a decrease in absorbance of yellow pigment,oxidant H2 O2 has a certain hyperchromic effect to the pigment.

  4. Powerful chemical technique. [CSIR uses new x-ray diffractometer for structural chemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    The CSIR's National Chemical Research Laboratory (NCRL) is now using one of the most powerful techniques available to determine the structure of molecules. It has recently acquired a Single Crystal X-ray Diffractometer. This powerful method provides the only means of determining the structure of certain compounds. NCRL scientists often carry out structure determinations to find out the relative or absolute stereochemistry of molecules. This is important when correlating physiological activity and structure, information which is necessary for synthesizing medicines with specific characteristics.

  5. Changes in the structure and pigmentation of the eyes of honeybee (Apis mellifera L. queens with the "limão" mutation

    Directory of Open Access Journals (Sweden)

    José Chaud-Netto

    2000-03-01

    Full Text Available This study describes the ultrastructural differences between the compound eyes of ch li/ch li and Ch/ch li honeybee queens. Heterozygous "limão" bees had an almost normal ultrastructural organization of the ommatidia, but there were some alterations, including small vacuoles in the crystalline cones and a loss of pigment by primary pigmentary cells. In homozygous bees many ommatidia had very deformed crystalline cones and there were some bipartite rhabdoma. There was a reduction in the amount of pigment in the primary and secondary pigmentary cells and receptor cells (retinulae of mutant eyes. However, the eyes of both heterozygous and homozygous queens had the same type of pigment granules. Certain membrane-limited structures containing pigment granules and electron-dense material appeared to be of lysosomal nature. Since these structures occurred in the retinular cells of mutant eyes, they were considered to be multivesicular bodies responsible for the reduction in rhabdom volume in the presence of light, as a type of adaptation to brightness. The reduction of pigment in the pigmentary and retinular cells and the morphological changes seen in the rhabdom of the ommatidia may originate visual deficiencies, which could explain the behavioral modifications reported for Apis mellifera queens with mutant eye color.Este estudo descreve as diferenças ultra-estruturais entre os olhos compostos de rainhas de abelhas de genótipo ch li/ch li e Ch/ch li. Foram registradas diferenças na organização do omatídeo e na pigmentação geral dos dois tipos de olhos. As abelhas heterozigotas apresentaram organização ultra-estrutural dos omatídeos praticamente normal. Contudo, foram observadas algumas alterações nos cones cristalinos, particularmente a presença de pequenos vacúolos nas células dos cones e perda de pigmento pelas células pigmentares primárias. Nas abelhas homozigotas foram encontrados vários omatídeos com cones cristalinos muito

  6. Rule-Based Classification of Chemical Structures by Scaffold.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Varin, Thibault

    2011-08-01

    Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.

  7. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  8. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  9. Semiquantitative and quantitative measurements for EDXRF in elemental chemical composition of pigments; Medidas semi-quantitativas e quantitativas por EDXRF em composicao quimica elementar de pigmentos

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Elizabeth Cristina Soares da

    2005-02-15

    X-Ray fluorescence technique is largely used in the characterization of art and archaeological objects for restoration and conservation, allowing a multi-elemental, simultaneous and non destructive analysis. In this work it was used a portable XRF equipment of XRF that consists of a {sup 238} Pu source ( 13,6 and 17,2 keV; 95 mCi) and a SI-PIN detector coupled to a 8 k multichannel analyser. The results were collected by a palmtop computer and later analysed in a PC, through the program AXIL-QXAS. The acquisition time for each measurement was 500 s. The measurements were accomplished in a wood sculpture (Santa Luzia image, number 164) from the collection of the Museu de Etnologia da Universidade de Sao Paulo (MAE-USP), in the following regions: (STL1) inferior side of the wood base exposed without finishing, (STL2) frontal inferior base of the pedestal (dark blue) (STL3), inferior part of the frontal dress (gold), (STL4) medium part of the dress (clear blue) (STL5) mantle (red), (STL6) back central lock of the hair in the backs (black), (STL7) right cheek (flesh-coloured) and (STL8) mantle (gold). The elements found in the STL1 region were: Al, Ca, Fe and a high concentration of Zn. In the region STL2 were found Al, C, Fe, Zn and the key element Cu. In the region STL3 - Ca, Zn and the key element Au. In the region STL4 it was found Zn and the key element Cu. In the region STL5 the key element S and Hg. In the region STL6 were found Fe, Ca, S and Hg. In the region STL 7 were found Al, Cu, Hg and Zn. In the region STL8 were found Ca, Al and Au, with high concentration. It was concluded that the possible pigments would be: STL2 and STL4 - CuCO{sub 3}. Cu(OH){sub 2} + ZnO; STL3 and STL8 - Au; STL5 - HgS, STL6 - HgS mixed with other oxides, possibly of Fe and Mn, and STL 7 - HgS + ZnO. Standard samples of wood painted with pigments of the colors white, blue, red, rose, flesh color and green were also made. Through the XRF method it was verified that the white pigment is

  10. Production and biological activities of yellow pigments from Monascus fungi.

    Science.gov (United States)

    Chen, Gong; Wu, Zhenqiang

    2016-08-01

    Monascus yellow pigments (MYPs), are azaphilone compounds and one of the three main components of total Monascus pigments (MPs). Thirty-five hydrophilic or hydrophobic MYPs have been identified, with the majority being hydrophobic. Apart from screening special Monascus strains, some advanced approaches, such as extractive and high-cell-density fermentations, have been applied for developing or producing new MYPs, especially extracellular hydrophilic MYPs. The outstanding performance of MYPs in terms of resistance to photodegradation, as well as tolerance for temperature and pH, give natural MYPs reasonable prospects, compared with the orange and red MPs, for practical use in the present and future. Meanwhile, MYPs have shown promising potential for applications in the food and pharmaceutical industries based on their described bioactivities. This review briefly summarizes the reports to date on chemical structures, biological activities, biosynthetic pathways, production technologies, and physicochemical performances of MYPs. The existing problems for MYPs are discussed and research prospects proposed.

  11. Analysis of gallstone composition and structure in Jharkhand region.

    Science.gov (United States)

    Sharma, Rajani; Soy, Snehi; Kumar, Chandan; Sachan, Shashwati Ghosh; Sharma, Shubha Rani

    2015-01-01

    The aim of this study was to analyze gallstones structurally and chemically as this may help to direct the measures for its treatment. On the basis of morphology, 459 gallstones were categorized into pigmented, cholesterol, and mixed gallstones and analyzed for their chemical structure and composition. Elementary analysis was done with the help of inductively coupled plasma, optical emission spectrophotometry. Fourier transform infrared spectroscopy was used for compound analysis. The effects of thermal stability were analyzed by thermal gravimetric analysis (TGA). Statistical analysis was done to correlate gallstone composition with their shape and number in gallbladder. Pigmented gallstones were predominant and generally occurred in multiple forms, cholesterol as solitaire and black pigmented as slug (χ (2) = 3.56; p gallstones while pigmented gallstones were more compact in structure. Both types of structure were seen in mixed stones while black pigmented stones were amorphous in nature. This difference in structures might be due to difference in chemical compositions. Cholesterol and mixed stones contained basically cholesterol, brown pigmented constituted bilirubin as a major component, and black stones differed from brown pigmented stones by the presence of Ca palmitate. Bilirubin and palmitate were thermally more stable than cholesterol; hence pigmented gallstones were thermally more stable than cholesterol gallstones, as seen in TGA study. Pigmented gallstones were most common in this study of gallstones from the Jharkhand region.

  12. Structure activity relationships to assess new chemicals under TSCA

    Energy Technology Data Exchange (ETDEWEB)

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  13. Global Materials Structure Search with Chemically Motivated Coordinates.

    Science.gov (United States)

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

  14. Análise química de pigmentos minerais naturais de Itabirito (MG Chemical analysis on natural mineral pigments from Itabirito (MG

    Directory of Open Access Journals (Sweden)

    A. R. P. Pereira

    2007-03-01

    Full Text Available Este trabalho tem o propósito de estudar composições e aplicações de pigmentos de Minas Gerais. Foi realizado um estudo qualitativo e quantitativo de pigmentos naturais coletados na região de Itabirito. As amostras foram denominadas segundo o Sistema Munsell de Cores e apresentaram composições variadas. Os minerais identificados por difração de raios X e confirmados por microscopia eletrônica de varredura (MEV foram a caulinita, ilita, talco e hematita, característicos da região. Análises de espectroscopia dispersiva de energia (EDS produziram resultados semi-quantitativos dos elementos presentes. A termogravimetria indicou pequena perda de massa, referente à umidade das amostras. A análise térmica diferencial indicou uma quantidade maior de caulinita no pigmento vermelho em relação aos demais. O teor de ferro presente nas amostras foi determinado por análise volumétrica e por espectrofotometria por absorção molecular na região do ultravioleta-visível. Os pigmentos apresentaram boa estabilidade térmica indicando a sua potencialidade de aplicação em peças cerâmicas.This work has the purpose of studying compositions and applications of natural pigments found in Minas Gerais. A qualitative and quantitative study of some pigments collected in the region of Itabirito was carried out. The samples were named according to Munsell Color System and presented a variety of compositions. The minerals identified by X-ray diffraction and confirmed by scanning electronic microscopy (SEM were kaolinite, illite, talc and hematite, characteristic from this region. Analyses by energy dispersive spectroscopy (EDS produced semi-quantitative results of the elements present in the samples. Thermogravimetry indicated small weight loss referring to the humidity of the samples. Differential thermal analysis indicated a large amount of kaolinite in the red pigment when compared with the others. The iron content presents in the samples was

  15. Structure of adsorbed monolayers. The surface chemical bond

    Energy Technology Data Exchange (ETDEWEB)

    Somorjai, G.A.; Bent, B.E.

    1984-06-01

    This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table.

  16. Dissolution rate measurements of sea water soluble pigments for antifouling paints

    DEFF Research Database (Denmark)

    Yebra, Diego Meseguer; Kiil, Søren; Erik Weinell, Claus

    2006-01-01

    The dissolution of soluble pigments from both tin-based and tin-free chemically active antifouling (AF) paints is a key process influencing their polishing and biocide leaching rates. In this context, a low time- and resources-consuming method capable of screening the pigment behaviour in the sea......The dissolution of soluble pigments from both tin-based and tin-free chemically active antifouling (AF) paints is a key process influencing their polishing and biocide leaching rates. In this context, a low time- and resources-consuming method capable of screening the pigment behaviour...... in the search for the most promising materials or mixtures is of great interest. A preliminary attempt to develop such a method is presented in this paper based on the widely used ZnO pigments. While highly pure, nano-polished, monocrystalline ZnO substrates yielded very low dissolution rates in the order of 17...... of defects in the lattice structure, are hypothesised to be responsible for the faster sea water attack of the pellets compared to the ZnO crystals. In any case, the ZnO dissolution rates reported in this paper are markedly lower than those associated with the sea water dissolution of cuprous oxide (Cu2O...

  17. Composição química dos cascos de eqüinos das raças Pantaneira e Mangalarga Marchador Chemical composition of black versus non-pigmented hooves from Pantaneira and Mangalarga Marchador horses

    Directory of Open Access Journals (Sweden)

    G.A. Faria

    2005-10-01

    Full Text Available Pesquisaram-se eventuais diferenças na composição da matéria seca (MS, proteína bruta, extrato etéreo, cinzas, cálcio, fósforo, cobre, zinco, perfil de aminoácidos e biotina entre cascos pretos e claros, de eqüinos das raças Pantaneira e Mangalarga Marchador, criados na região do Pantanal, MS, e no município de Caeté, MG, respectivamente. De cada raça foram coletadas amostras de 10 éguas vazias, não lactantes, com idade entre 5 e 10 anos, sendo que, em um mesmo animal, foram retiradas amostras das duas colorações de casco nas regiões da pinça, ombro, quarto e talão. Na raça Pantaneira, os cascos claros apresentaram maior teor de fósforo que os pretos, e os demais elementos avaliados não foram diferentes segundo a cor. Na Mangalarga Marchador, não houve diferença entre os cascos claros e pretos, quanto a todas as características estudadas.Chemical composition (dry matter, crude protein, ether extract, ash, calcium, phosphorus, copper and zinc and amino acid profile in black and non-pigmented hooves from non-lactating five-to ten-year-old Pantaneira and Mangalarga Marchador mares raised in central and southeastern Brazil was studied. In the Pantaneira breed, phosphorus concentration was higher in non-pigmented than in black hooves, but hoof color did not affect any other composition variables. Likewise, black versus non-pigmented hooves did not differ for any composition variable in the Mangalarga Marchador mares.

  18. Study of the pigments elementary chemical composition of a painting in process of attribution to Gainsborough employing a portable X-rays fluorescence system

    Science.gov (United States)

    Appoloni, C. R.; Blonski, M. S.; Parreira, P. S.; Souza, L. A. C.

    2007-09-01

    The investigated painting, named as "The woodman" by its owners, is in process of authenticity verification as a Thomas Gainsborough (XVIII century) painting and is under investigation at the Laboratory of Conservation Science (LACICOR), CECOR/EBA/UFMG. The authentication process is still in course. The measurements were carried out in the place where the painting was on custody, with a portable X-rays fluorescence (XRF) system constituted of a X-rays tube with Ag anode, a Si-PIN diode detector, nuclear electronic chain and a specially designed mechanical system for the detector and X-rays tube positioning, that enables angular and XYZ movements of the excitation-detection system. The employed voltage and current intensity of the X-rays tube were 17 kV and 3 μA, respectively. The time of acquisition for each measurement was 500 s. XRF spectra were analyzed using the AXIL-WinQXAS software. Three measurements in each of the following regions of the painting were done: face, leaves, arm, sky and firewood. The carried out analysis indicated the following pigments: White (lead white and calcium sulfate, identified by the elements Pb, Ca and S), Blue (Prussian blue, identified by the key element Fe), Red (Vermilion, identified by the elements Hg and S) and Brown (mixture of Fe and Mn oxides, identified by the elements Fe and Mn). Elements belonging to modern pigments (after XVIII century) corresponding to the same colors were absent in the analyzed spectra.

  19. Holographic films from carotenoid pigments

    Science.gov (United States)

    Toxqui-López, S.; Lecona-Sánchez, J. F.; Santacruz-Vázquez, C.; Olivares-Pérez, A.; Fuentes-Tapia, I.

    2014-02-01

    Carotenoids pigments presents in pineapple can be more than just natural dyes, which is one of the applications that now at day gives the chemical industry. In this research shown that can be used in implementing of holographic recording Films. Therefore we describe the technique how to obtain this kind of pigments trough spay drying of natural pineapple juice, which are then dissolved with water in a proportion of 0.1g to 1mL. The obtained sample is poured into glass substrates using the gravity method, after a drying of 24 hours in laboratory normal conditions the films are ready. The films are characterized by recording transmission holographic gratings (LSR 445 NL 445 nm) and measuring the diffraction efficiency holographic parameter. This recording material has good diffraction efficiency and environmental stability.

  20. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  1. Applications of the Cambridge Structural Database in chemical education1

    Science.gov (United States)

    Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

    2010-01-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  2. AUTOMATED DETECTION OF STRUCTURAL ALERTS (CHEMICAL FRAGMENTS IN (ECOTOXICOLOGY

    Directory of Open Access Journals (Sweden)

    Alban Lepailleur

    2013-02-01

    Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

  3. Computational analysis of RNA structures with chemical probing data.

    Science.gov (United States)

    Ge, Ping; Zhang, Shaojie

    2015-06-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.

  4. Protein secondary structure prediction using NMR chemical shift data.

    Science.gov (United States)

    Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

    2010-10-01

    Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

  5. Characterization of iron-phosphate-silicate chemical garden structures.

    Science.gov (United States)

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  6. Expression Differences of Pigment Structural Genes and Transcription Factors Explain Flesh Coloration in Three Contrasting Kiwifruit Cultivars

    Directory of Open Access Journals (Sweden)

    Yanfei Liu

    2017-09-01

    Full Text Available Fruits of kiwifruit cultivars (Actinidia chinensis and A. deliciosa generally have green or yellow flesh when ripe. A small number of genotypes have red flesh but this coloration is usually restricted to the inner pericarp. Three kiwifruit cultivars having red (‘Hongyang’, or yellow (‘Jinnong-2’, or green (‘Hayward’ flesh were investigated for their color characteristics and pigment contents during development and ripening. The results show the yellow of the ‘Jinnong-2’ fruit is due to the combined effects of chlorophyll degradation and of beta-carotene accumulation. The red inner pericarps of ‘Hongyang’ fruit are due to anthocyanin accumulation. Expression differences of the pathway genes in the inner pericarps of the three different kiwifruits suggest that stay-green (SGR controls the degradation of chlorophylls, while lycopene beta-cyclase (LCY-β controls the biosynthesis of beta-carotene. The abundance of anthocyanin in the inner pericarps of the ‘Hongyang’ fruit is the results of high expressions of UDP flavonoid glycosyltransferases (UFGT. At the same time, expressions of anthocyanin transcription factors show that AcMYBF110 expression parallels changes in anthocyanin concentration, so seems to be a key R2R3 MYB, regulating anthocyanin biosynthesis. Further, transient color assays reveal that AcMYBF110 can autonomously induce anthocyanin accumulation in Nicotiana tabacum leaves by activating the transcription of dihydroflavonol 4-reductase (NtDFR, anthocyanidin synthase (NtANS and NtUFGT. For basic helix-loop-helix proteins (bHLHs and WD-repeat proteins (WD40s, expression differences show these may depend on AcMYBF110 forming a MYB-bHLH-WD40 complex to regulate anthocyanin biosynthesis, instead of it having a direct involvement.

  7. Ultraviolet vision in lacertid lizards: evidence from retinal structure, eye transmittance, SWS1 visual pigment genes and behaviour.

    Science.gov (United States)

    Pérez i de Lanuza, Guillem; Font, Enrique

    2014-08-15

    Ultraviolet (UV) vision and UV colour patches have been reported in a wide range of taxa and are increasingly appreciated as an integral part of vertebrate visual perception and communication systems. Previous studies with Lacertidae, a lizard family with diverse and complex coloration, have revealed the existence of UV-reflecting patches that may function as social signals. However, confirmation of the signalling role of UV coloration requires demonstrating that the lizards are capable of vision in the UV waveband. Here we use a multidisciplinary approach to characterize the visual sensitivity of a diverse sample of lacertid species. Spectral transmission measurements of the ocular media show that wavelengths down to 300 nm are transmitted in all the species sampled. Four retinal oil droplet types can be identified in the lacertid retina. Two types are pigmented and two are colourless. Fluorescence microscopy reveals that a type of colourless droplet is UV-transmitting and may thus be associated with UV-sensitive cones. DNA sequencing shows that lacertids have a functional SWS1 opsin, very similar at 13 critical sites to that in the presumed ancestral vertebrate (which was UV sensitive) and other UV-sensitive lizards. Finally, males of Podarcis muralis are capable of discriminating between two views of the same stimulus that differ only in the presence/absence of UV radiance. Taken together, these results provide convergent evidence of UV vision in lacertids, very likely by means of an independent photopigment. Moreover, the presence of four oil droplet types suggests that lacertids have a four-cone colour vision system.

  8. Chemical and structural effects of base modifications in messenger RNA

    Science.gov (United States)

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles.

  9. Review of Prodigiosin, Pigmentation in Serratia marcescens

    Directory of Open Access Journals (Sweden)

    Anita Khanafari

    2006-01-01

    Full Text Available Prodigiosins, a family of natural red pigments characterized by a common pyrrolylpyrromethane skeleton, are produced by various bacteria that first characterized from Serratia marcescens. This pigment is a promising drug owing to its reported characteristics of having antifungal, immunosuppressive and anti-proliferative activity. From an industrial point of view to obtain optimal conditions to enhance the growth of Serratia marcescens and the pigment production is necessity. In present study, the production condition, physicochemical and functional characteristics, structure, genetic and gene expression, apoptosis and toxigenic effects of prodigiosin will be discussed in-order to contribute to the world of Serratia marcescens with respect to its prodigiosin production property.

  10. Chemical compatibility of structural materials in alkali metals

    Energy Technology Data Exchange (ETDEWEB)

    Natesan, K.; Rink, D.L.; Haglund, R. [Argonne National Lab., Chicago, IL (United States)] [and others

    1995-04-01

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments.

  11. Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

    DEFF Research Database (Denmark)

    Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim

    2013-01-01

    Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of tw......)-roseoside (4), and one glutinane type triterpene, epi-glutinol (5), from the leaves of T. tagetiflora. Their structures are established by 1D and 2D NMR spectroscopy, as well as ESI-MS analysis and comparison with literature data...

  12. Screening of Marine Actinomycetes from Segara Anakan for Natural Pigment and Hydrolytic Activities

    Science.gov (United States)

    Asnani, A.; Ryandini, D.; Suwandri

    2016-02-01

    Marine actinomycetes have become sources of great interest to natural product chemistry due to their new chemical entities and bioactive metabolites. Since April 2010, we have screened actinobacteria from five sites that represent different ecosystems of Segara Anakan lagoon. In this present study we focus on specific isolates, K-2C which covers 1) actinomycetes identification based on morphology observation and 16S rRNA gene; 2) fermentation and isolation of pigment; 3) structure determination of pigment; and 4) hydrolytic enzymes characterization; Methodologies relevant to the studies were implemented accordingly. The results indicated that K-2C was likely Streptomyces fradiae strain RSU15, and the best fermentation medium should contain starch and casein with 21 days of incubation. The isolate has extracellular as well as intracellular pigments. Isolated pigments gave purple color with λmax of 529.00 nm. The pigment was structurally characterized. Interestingly, Streptomyces K-2C was able to produce potential hydrolytic enzymes such as amylase, cellulase, protease, lipase, urease, and nitrate reductase.

  13. Design of LTCC-based Ceramic Structure for Chemical Microreactor

    Directory of Open Access Journals (Sweden)

    D. Belavic

    2012-04-01

    Full Text Available The design of ceramic chemical microreactor for the production of hydrogen needed in portable polymer-electrolyte membrane (PEM fuel cells is presented. The microreactor was developed for the steam reforming of liquid fuels with water into hydrogen. The complex three-dimensional ceramic structure of the microreactor includes evaporator(s, mixer(s, reformer and combustor. Low-temperature co-fired ceramic (LTCC technology was used to fabricate the ceramic structures with buried cavities and channels, and thick-film technology was used to make electrical heaters, temperature sensors and pressure sensors. The final 3D ceramic structure consists of 45 LTCC tapes. The dimensions of the structure are 75 × 41 × 9 mm3 and the weight is about 73 g.

  14. 3,3'-Diindolylmethane inhibits VEGF expression through the HIF-1α and NF-κB pathways in human retinal pigment epithelial cells under chemical hypoxic conditions.

    Science.gov (United States)

    Park, Hongzoo; Lee, Dae-Sung; Yim, Mi-Jin; Choi, Yung Hyun; Park, Saegwang; Seo, Su-Kil; Choi, Jung Sik; Jang, Won Hee; Yea, Sung Su; Park, Won Sun; Lee, Chang-Min; Jung, Won-Kyo; Choi, Il-Whan

    2015-07-01

    Oxidative stress in the retinal pigment epithelium (RPE) can lead to the pathological causes of age-related macular degeneration (AMD). Hypoxia induces oxidative damage in retinal pigment epithelial cells (RPE cells). In this study, we investigated the capacity of 3,3'-diindolylmethane (DIM) to reduce the expression of vascular endothelial growth factor (VEGF) under hypoxic conditions, as well as the molecular mechanisms involved. Human RPE cells (ARPE-19 cells) were treated with cobalt chloride (CoCl2, 200 µM) and/or DIM (10 and 20 µM). The production of VEGF was measured by enzyme-linked immunosorbent assay. The translocation of hypoxia-inducible factor-1α (HIF-1α) and nuclear factor-κB (NF-κB) was determined by western blot analysis. The binding activity of HIF-1α and NF-κB was analyzed by electrophoretic mobility shift assay. The phosphorylation levels of mitogen-activated protein kinases (MAPKs) were measured by western blot analysis. The levels of mitochondrial reactive oxygen species (ROS) were detected by fluorescence microplate assay. The results revealed that DIM significantly attenuated the CoCl2-induced expression of VEGF in the ARPE-19 cells. The CoCl2-induced translocation and activation of HIF-1α and NF-κB were also attenuated by treatment with DIM. In addition, DIM inhibited the CoCl2-induced activation of p38 MAPK in the ARPE-19 cells. Pre-treatment with YCG063, a mitochondrial ROS inhibitor, led to the downregulation of the CoCl2-induced production of VEGF by suppressing HIF-1α and NF-κB activity. Taken together, the findings of our study demonstrate that DIM inhibits the CoCl2-induced production of VEGF by suppressing mitochondrial ROS production, thus attenuating the activation of HIF-1α and p38 MAPK/NF-κB.

  15. Shock-Induced Chemical Reactions in Structural Energetic Materials

    Science.gov (United States)

    Narayanan, V.; Lu, X.; Hanagud, S.

    2006-07-01

    Various powder mixtures like intermetallic mixtures and mixtures of metals and metal oxides have potential applications as structural energetic materials (SEMs). Technologies of varying the compositions and the powder sizes and their synthesis are being investigated to provide multiple desirable characteristics, like high strength and high energy content. In this paper, we formulate a model for SEMs for their application in shock conditions, in the framework of nonequilibrium thermodynamics and continuum mechanics. A mixture of Al and KClO4 is selected as the example for SEMs. A mixture, pore collapse and chemical reaction model are included. By adapting energy barriers for reaction as a function of temperature, particle size and pressure and introducing a relaxation mechanism in the reaction model, a shock-induced chemical reaction model is developed. The variation of the relaxation mechanism is also modeled. The initiation and propagation of chemical reactions are studied. The time and spatial dependency of chemical reaction on the shock wave conditions are investigated.

  16. Chemical and physical structures of proteinoids and related polyamino acids

    Science.gov (United States)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  17. Chemical structure analysis of starch and cellulose derivatives.

    Science.gov (United States)

    Mischnick, Petra; Momcilovic, Dane

    2010-01-01

    Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch and cellulose cause the products resulting from their modification to display high complexity. Chemical composition analysis of these mixtures is therefore a challenging task. Detailed knowledge on substitution patterns is fundamental for understanding structure-property relationships in modified cellulose and starch, and thus also for the improvement of reproducibility and rational design of properties. Substitution patterns resulting from kinetically or thermodynamically controlled reactions show certain preferences for the three available hydroxyl functions in (1→4)-linked glucans. Spurlin, seventy years ago, was the first to describe this in an idealized model, and nowadays this model has been extended and related to the next hierarchical levels, namely, the substituent distribution in and over the polymer chains. This structural complexity, with its implications for data interpretation, and the analytical approaches developed for its investigation are outlined in this article. Strategies and methods for the determination of the average degree of substitution (DS), monomer composition, and substitution patterns at the polymer level are presented and discussed with respect to their limitations and interpretability. Nuclear magnetic resonance spectroscopy, chromatography, capillary electrophoresis, and modern mass spectrometry (MS), including tandem MS, are the main instrumental techniques employed, in combination with appropriate sample preparation by chemical and enzymatic methods.

  18. Chemical structure of odorants and perceptual similarity in ants.

    Science.gov (United States)

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity.

  19. The chemical structure and the crystalline structures of Bombyx mori silk fibroin.

    Science.gov (United States)

    Lotz, B; Colonna Cesari, F

    1979-01-01

    Some recent data (i.e. published in the last ten years) on the chemical and crystalline structures of B. mori silk are reviewed. The main emphasis is put on the crystallizable portion of silk fibroin, including its chemical constitution and its molecular conformation (at the crystallographic unit-cell level) in the two crystalline modifications : the beta pleated sheet and the silk I structures. The structural aspects are based on a discussion of X-ray and electron diffraction data, and on conformational energy analyses of a model (Ala-Gly)n polypeptide of silk fibroin.

  20. Linear complexions: Confined chemical and structural states at dislocations.

    Science.gov (United States)

    Kuzmina, M; Herbig, M; Ponge, D; Sandlöbes, S; Raabe, D

    2015-09-04

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  1. Chemically Resolved Structure of the Sn/Ge(111) Surface

    Science.gov (United States)

    Lee, Tien-Lin; Warren, Samantha; Cowie, Bruce C. C.; Zegenhagen, Jörg

    2006-02-01

    The structure and chemical states of the Sn/Ge(111) surface are characterized by x-ray standing waves combined with photoemission. For the room temperature 3×3 phase two chemical components, approximately 0.4 eV apart, are observed for both Sn 3d and 4d core levels. Our model-independent, x-ray standing wave analysis shows unambiguously that the two components originate from Sn adatoms located at two different heights separated vertically by 0.23 Å, in favor of a model composed of a fluctuating Sn layer. Contrary to the most accepted scenario, the stronger Sn 3d and 4d components, which appear at the lower binding-energy sides and account for 2/3 of the Sn adatoms, are identified to be associated with the higher Sn position, manifesting their filled valence state character.

  2. The double-layered chemical structure in DB white dwarfs

    CERN Document Server

    Althaus, L G

    2004-01-01

    We study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Our treatment of diffusion includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is characterized by a pure helium envelope atop an intermediate remnant shell rich in helium, carbon and oxygen, is expected for pulsating DB white dwarfs, assuming that they are descendants of hydrogen-deficient PG1159 post-AGB stars. We find that, depending on the stellar mass, if DB white dwarf progenitors are formed with a helium content smaller than \\approx 10^-3 M_*, a single-layered configuration is expected to emerge during the DB pulsation instability strip. We also explore the consequences of diffusively evolving ch...

  3. Preparation of blue pigment extract from pickled garlic and its physio-chemical properties%绿变大蒜蓝色素的制备及理化活性

    Institute of Scientific and Technical Information of China (English)

    赵晓丹; 李星

    2014-01-01

    为了进一步明确大蒜绿变物质的结构及性质,该研究对绿变产物进行分离制备并探索了其相关理化活性。从绿变大蒜中提取出绿变产物,并通过AmberliteCG-50和SephadexLH-20两步纯化制备得到了蓝色素的纯化产品,其色价为76.7。对色素的理化性质进行了研究,结果表明蓝色素在酸性条件pH值<7时稳定;对热处理也比较稳定,60℃以下加热处理对色素影响较小;长时间的日光照射会使蓝色素有较大的损失;一些常见的金属离子Cu2+、Zn2+、Al3+、Fe2+的存在对蓝绿色素几乎没有影响,Fe3+的存在会使色素迅速褪色。蓝色素对自由基有清除效果:质量浓度为2 mg/mL的蓝色素提取物对1,1-二苯基-2-三硝基苯肼(DPPH)清除率达到96.4%;在10 mg/mL质量浓度下,蓝色素对超氧和羟基自由基的清除率分别为96.8%和87.6%;色素提取物对自由基的清除效果低于同浓度的抗坏血酸。该研究结果对深入研究绿变色素的性质和结构奠定了初步基础。%The greening compounds in garlic are of great importance to both industry and academic research. In this study, the blue pigment extract in greening garlic has been prepared and its physio-chemical properties and scavenging activities towards DPPH radicals, superoxide anion radicals and hydroxyl radicals have been investigated. The blue pigments in Laba garlic were extracted and separated by chromatography with Amberlite CG-50 and Sephadex LH-20, and the blue pigment extract (BPE) was obtained. Color value of BPE was elevated to 76.7 compared to 10.7 that of the raw extract without any purification. BPE was stable in acidic conditions, but sensitive to illumination. Low-temperature heating (lower than 60 2℃+,)Zhna2d+,lAittl3e+,eFffe2c+thoandthliettlsetaebfifleictyt onfBthPeE.M etalionssuch as pigment stability, but Fe3+ caused obvious color loss. The BPE displayed concentration-dependent inhibition of 1,1-diphenyl

  4. Pigments of fly agaric (Amanita muscaria).

    Science.gov (United States)

    Stintzing, Florian; Schliemann, Willibald

    2007-01-01

    The complex pigment pattern of fly agaric (Amanita muscaria) cap skins has been studied by LC-DAD and mass spectrometry. Among the betaxanthins the corresponding derivatives of serine, threonine, ethanolamine, alanine, Dopa, phenylalanine and tryptophan are reported for the first time to contribute to the pigment pattern of fly agarics. Betalamic acid, the chromophoric precursor of betaxanthins and betacyanins, muscaflavin and seco-dopas were also detected. Furthermore, the red-purple muscapurpurin and the red muscarubrin were tentatively assigned while further six betacyanin-like components could not be structurally allocated. Stability studies indicated a high susceptibility of pigment extracts to degradation which led to rapid colour loss thus rendering a complete characterization of betacyanin-like compounds impossible at present. Taking into account these difficulties the presented results may be a starting point for a comprehensive characterization of the pigment composition of fly agarics.

  5. Organic Semiconductors based on Dyes and Color Pigments.

    Science.gov (United States)

    Gsänger, Marcel; Bialas, David; Huang, Lizhen; Stolte, Matthias; Würthner, Frank

    2016-05-01

    Organic dyes and pigments constitute a large class of industrial products. The utilization of these compounds in the field of organic electronics is reviewed with particular emphasis on organic field-effect transistors. It is shown that for most major classes of industrial dyes and pigments, i.e., phthalocyanines, perylene and naphthalene diimides, diketopyrrolopyrroles, indigos and isoindigos, squaraines, and merocyanines, charge-carrier mobilities exceeding 1 cm(2) V(-1) s(-1) have been achieved. The most widely investigated molecules due to their n-channel operation are perylene and naphthalene diimides, for which even values close to 10 cm(2) V(-1) s(-1) have been demonstrated. The fact that all of these π-conjugated colorants contain polar substituents leading to strongly quadrupolar or even dipolar molecules suggests that indeed a much larger structural space shows promise for the design of organic semiconductor molecules than was considered in this field traditionally. In particular, because many of these dye and pigment chromophores demonstrate excellent thermal and (photo-)chemical stability in their original applications in dyeing and printing, and are accessible by straightforward synthetic protocols, they bear a particularly high potential for commercial applications in the area of organic electronics.

  6. Boron-containing organic pigments from a Jurassic red alga

    Science.gov (United States)

    Wolkenstein, Klaus; Gross, Jürgen H.; Falk, Heinz

    2010-01-01

    Organic biomolecules that have retained their basic chemical structures over geological periods (molecular fossils) occur in a wide range of geological samples and provide valuable paleobiological, paleoenvironmental, and geochemical information not attainable from other sources. In rare cases, such compounds are even preserved with their specific functional groups and still occur within the organisms that produced them, providing direct information on the biochemical inventory of extinct organisms and their possible evolutionary relationships. Here we report the discovery of an exceptional group of boron-containing compounds, the borolithochromes, causing the distinct pink coloration of well-preserved specimens of the Jurassic red alga Solenopora jurassica. The borolithochromes are characterized as complicated spiroborates (boric acid esters) with two phenolic moieties as boron ligands, representing a unique class of fossil organic pigments. The chiroptical properties of the pigments unequivocally demonstrate a biogenic origin, at least of their ligands. However, although the borolithochromes originated from a fossil red alga, no analogy with hitherto known present-day red algal pigments was found. The occurrence of the borolithochromes or their possible diagenetic products in the fossil record may provide additional information on the classification and phylogeny of fossil calcareous algae. PMID:20974956

  7. EFFECT OF CHEMICAL STRUCTURE OF POLYCARBONATES ON ENTANGLEMENT SPACING

    Institute of Scientific and Technical Information of China (English)

    Wei Ning; Wen-xiang Zhu; Bao-qing Zhang; Chun-cheng Li; Chen-yang Liu; Du-jin Wang

    2012-01-01

    The master curves of a series of aliphatic polycarbonates (APCs) with different lengths of methylene segments in the repeat unit were obtained by dynamic rheological measurements.The plateau modulus and entanglement molecular weight were determined and cross-checked by different methods.Though having distinct difference in chemical structure of repeat units,both APCs and bisphenol-A polycarbonates have the similar entanglement weight and entanglement spacing.On the other side,the plateau modulus decreases with increasing the length of the side group of atiphatic polycarbonates with different side-chain lengths in the literature.The packing length model can explain the relationship between chain structure and entanglements.

  8. Characterization of phytoplankton pigments and functional community structure in the Gulf of Mannar and the Palk Bay using HPLC–CHEMTAX analysis.

    Digital Repository Service at National Institute of Oceanography (India)

    Madhu, N.V.; Ullas, N.; Ashwini, R.; Meenu, P.; Rehitha, T.V.; Lallu, K.R.

    , zeaxanthin, and alloxanthin) are diagnostic of specific phytoplankton functional groups (diatoms,dinoflagellates,chlorophytes, cyanobacteria and cryptophytes, respectively) and in a few cases can determine phytoplankton composition at the species level...., 2012). The diagnostic pigment (DP) criteria derived from different combinations of marker pigments (Table 1), roughly corresponds to the biomass proportions of various size groups (pico-, nano- and micro-) of phytoplankton (Vidussi et al., 2001...

  9. GREEN FLUORESCENT PIGMENT ACCUMULATED BY A MUTANT OF CELLVIBRIO GILVUS.

    Science.gov (United States)

    LOVE, S H; HULCHER, F H

    1964-01-01

    Love, Samuel H. (Bowman Gray School of Medicine, Winston-Salem, N.C.), and Frank H. Hulcher. Green fluorescent pigment accumulated by a mutant of Cellvibrio gilvus. J. Bacteriol. 87:39-45. 1964.-A mutant of Cellvibrio gilvus, designated strain 139A, liberated a green, fluorescent pigment into the surrounding culture medium. A study of the factors which affected the accumulation of this pigment led to the development of a chemically defined medium which supported maximal pigment accumulation in aerated, liquid cultures. d-Glucose, glycine or l-serine, l-phenylalanine, l-proline, and l-lysine comprised the organic components of this medium. The visible absorption spectrum of the pigment showed a maximal band at 400 mmu (pH 7.0). A difference spectrum between reduced and oxidized pigment showed loss of the band at 400 mmu upon oxidation. However, a methanol-extractable, flavinelike compound occurred in the wild strain but not in the mutant. Ferric ions added to the defined medium stimulated growth, with a concomitant reduction of pigment accumulation. Pigment was formed at a maximal rate during the stationary growth phase, and the highest yield was obtained by 18 hr. Organic solvents did not extract the pigment from water solutions. One and sometimes two, compounds absorbing at 400 mmu could be eluted by ion-exchange chromatography on Cellex-P (H(+)), which was used to separate the pigment from other components in the culture supernatants so that the radioactivity of the pigment could be measured. The mutant synthesized C(14)-labeled pigment from d-glucose-U-C(14) and from each of four amino acids (glycine-1-C(14), l-phenylalanine-U-C(14), l-proline-U-C(14), and l-lysine-U-C(14). Delta-Amino-levulenic acid-4-C(14) did not contribute C(14) to the pigment.

  10. Structural damage and chemical contaminants on reprocessed arthroscopic shaver blades.

    Science.gov (United States)

    Kobayashi, Masahiko; Nakagawa, Yasuaki; Okamoto, Yukihiro; Nakamura, Shinichiro; Nakamura, Takashi

    2009-02-01

    In response to socioeconomic pressure to cut budgets in medicine, single-use surgical instruments are often reprocessed despite potential biological hazard. To evaluate the quality and contaminants of reprocessed shaver blades. Reprocessed shaver blades have mechanical damage and chemical contamination. Controlled laboratory study. Seven blades and 3 abraders were reprocessed 1 time or 3 times and then were assessed. In the first part of the study, structural damage on the blades after 3 reprocessings was compared to that after 1 reprocessing using optical microscopy. In the second part, surface damage was observed using optical microscopy and scanning electron microscopy; elemental and chemical analyses of contaminants found by the microscopy were performed using scanning electron microscopy/energy dispersive x-ray spectroscopy, scanning Auger microscopy, and Fourier transform infrared spectroscopy. Optical microscopic examination revealed abrasion on the surface of the inner blade and cracks on the inner tube after 1 reprocessing. These changes were more evident after 3 reprocessings. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the blade reprocessed once showed contaminants containing calcium, carbon, oxygen, and silicon, and Fourier transform infrared spectroscopy demonstrated biological protein consisting mainly of collagen, some type of salts, and polycarbonate used in plastic molding. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the reprocessed abrader revealed contaminants containing carbon, calcium, phosphorous, and oxygen, and Fourier transform infrared spectroscopy showed H2O, hydroxyapatite, and hydroxyl proteins. Scanning Auger microscopy showed that the tin-nickel plating on the moving blade and abrader was missing in some locations. This is the first study to evaluate both mechanical damage and chemical contaminants containing collagen, hydroxyapatite, and salts

  11. Pigments in Thermophilic fungi

    OpenAIRE

    Somasundaram, T.; Rao, Sanjay SR; Maheshwari,R.

    1986-01-01

    UV and visible absorption spectra of thermophilic fungi were obtained by photoacoustic spectroscopy. Based on these data as well as on the chem. properties and IR spectra, it is suggested that the pigments may be hydroxylated polycyclic quinones.

  12. Shock induced chemical reactions in energetic structural materials

    Science.gov (United States)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  13. Photosynthetic Pigments in Diatoms

    OpenAIRE

    Paulina Kuczynska; Malgorzata Jemiola-Rzeminska; Kazimierz Strzalka

    2015-01-01

    Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvestin...

  14. Graph-based pigment network detection in skin images

    Science.gov (United States)

    Sadeghi, M.; Razmara, M.; Ester, M.; Lee, T. K.; Atkins, M. S.

    2010-03-01

    Detecting pigmented network is a crucial step for melanoma diagnosis. In this paper, we present a novel graphbased pigment network detection method that can find and visualize round structures belonging to the pigment network. After finding sharp changes of the luminance image by an edge detection function, the resulting binary image is converted to a graph, and then all cyclic sub-graphs are detected. Theses cycles represent meshes that belong to the pigment network. Then, we create a new graph of the cyclic structures based on their distance. According to the density ratio of the new graph of the pigment network, the image is classified as "Absent" or "Present". Being Present means that a pigment network is detected in the skin lesion. Using this approach, we achieved an accuracy of 92.6% on five hundred unseen images.

  15. Molecular Dynamics Simulation and Experimental Studies on the Visual Pigment Rhodopsin: Multiple Conformational States and Structural Changes

    CERN Document Server

    Kholmurodov, Kh T; Ostrovsky, M A; Biochemical Physics Institute, Russian Academy of Sciences, Moscow, Russia

    2005-01-01

    Based on the MD simulations with a supercomputer and the special-purposes MDGRAPE-2 machine we have performed 3-ns MD calculations on the rhodopsin molecule and presented the structure analysis data for its dark-adapted state. We have fulfilled the RMSD (root-mean-square deviation) and structural analysis for the rhodopsin (with 11-\\textit{cis} retinal), generated the pictures of the atomic-scale processes for the binding pocket, surrounding the chromophore retinal, and compared the helical deviations for the beta-ionone ring and Schiff base linkage regions of the protein. The most remarkable point of our observations is that the rhodopsin helical distortions in the dark state are accompanied with the transformation of the retinal chromophore, viz. with the rotation of the beta-ionone ring inside the protein binding pocket. The low-temperature absorption spectroscopy technique has been used to study the primary stages of rhodopsin photolysis. The structural transformation properties of rhodopsin were discusse...

  16. Modelling of structural effects on chemical reactions in turbulent flows

    Energy Technology Data Exchange (ETDEWEB)

    Gammelsaeter, H.R.

    1997-12-31

    Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

  17. 75 FR 38076 - Carbazole Violet Pigment 23 from India: Final Results of Antidumping Duty Administrative Review

    Science.gov (United States)

    2010-07-01

    ... receive a request for a hearing. \\1\\ Nation Ford Chemical Company and Sun Chemical Corporation. The period... the antidumping duty order is CVP 23 identified as Color Index No. 51319 and Chemical Abstract No... dry color. Pigment dispersions in any form (e.g., pigment dispersed in oleoresins, flammable...

  18. Proton beam modification of lead white pigments

    Energy Technology Data Exchange (ETDEWEB)

    Beck, L., E-mail: lucile.beck@cea.fr [CEA, DEN, Service de Recherches de Métallurgie Physique, Laboratoire JANNUS, 91191 Gif-sur-Yvette (France); Centre de recherche et de restauration des musées de France (C2RMF), Palais du Louvre – Porte des Lions, 14 quai François Mitterrand, 75001 Paris (France); Gutiérrez, P.C. [Centre de recherche et de restauration des musées de France (C2RMF), Palais du Louvre – Porte des Lions, 14 quai François Mitterrand, 75001 Paris (France); Centro de Micro-Análisis de Materiales (CMAM), Universidad Autónoma de Madrid, Campus de Cantoblanco, E-28049 Madrid (Spain); Miserque, F. [CEA, DEN, DPC/SCCME/LECA, 91191 Gif-sur-Yvette (France); Thomé, L. [Centre de Spectrométrie Nucléaire et de Spectrométrie de Masse (CSNSM), CNRS/IN2P3 et Université Paris-Sud, Bât. 108, 91405 Orsay (France)

    2013-07-15

    Pigments and paint materials are known to be sensitive to particle irradiation. Occasionally, the analysis of paintings by PIXE can induce a slight or dark stain depending on the experimental conditions (beam current, dose, particle energy). In order to understand this discoloration, we have irradiated various types of art white pigments – lead white (hydrocerussite and basic lead sulfate), gypsum, calcite, zinc oxide and titanium oxide – with an external 3 MeV proton micro-beam commonly used for PIXE experiments. We have observed various sensitivities depending on the pigment. No visible change occurs for calcite and titanium oxide, whereas lead white pigments are very sensitive. For the majority of the studied compounds, the discoloration is proportional to the beam current and charge. The damage induced by proton beam irradiation in lead white pigments was studied by micro-Raman and XPS spectroscopies. Structural modifications and dehydration were detected. Damage recovery was investigated by thermal treatment and UV-light irradiation. The discoloration disappeared after one week of UV illumination, showing that PIXE experiments could be safely undertaken for pigments and paintings.

  19. The influence of light intensity on anatomical structure and pigment contents of Tradescantia pallida (Rose Hunt. cv. purpurea Boom (Commelinaceae leaves

    Directory of Open Access Journals (Sweden)

    Élder Antonio Sousa Paiva

    2003-12-01

    Full Text Available The aim of this work was to study the effects of five different light intensities on the anatomical structure and on the pigment contents in leaves of Tradescantia pallida cv. purpurea. Once light intensity became lower, the thickness of leaf lamina and mesophyll were reduced. Adjustments in light-harvesting antenna size were observed: an increase in chlorophyll a + b/carotenoids ratio at low-light growth conditions. There was a strong positive linear correlation between the light intensity values and anthocyanin contents. Hence, T. pallida cv. purpurea acclimation to distinct environmental conditions might be related to its capacity of altering structurally and physiologically its phenotype.As espécies de Tradescantia colonizam uma ampla faixa de ambientes, desde aqueles completamente expostos a luz até aqueles caracteristicamente sombreados. Suas estratégias adaptativas e eficiência como invasoras de culturas estão provavelmente associadas a sua adaptação a intensidades luminosas distintas. Este trabalho mostra os efeitos de cinco diferentes intensidades luminosas na estrutura anatômica e no teor de pigmentos em folhas de Tradescantia pallida. As espessuras da lâmina foliar e do mesofilo foram alteradas, tornando-se mais delgadas à medida que a intensidade luminosa diminuiu. Observou-se um ajuste nos pigmentos fotossintéticos caracterizado por aumentos na razão clorofilas/carotenóides sob condições de baixa intensidade luminosa. Houve uma forte correlação linear positiva entre os valores de intensidade luminosa e teores de antocianinas. Deste modo, pode-se concluir que a aclimatação da espécie aos diferentes habitats está relacionada a alterações estruturais e fotossintéticas.

  20. Integrating chemical footprinting data into RNA secondary structure prediction.

    Directory of Open Access Journals (Sweden)

    Kourosh Zarringhalam

    Full Text Available Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension, yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints, which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

  1. Evolution of polymer photovoltaic performances from subtle chemical structure variations.

    Science.gov (United States)

    Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

    2012-11-21

    Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency.

  2. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    Directory of Open Access Journals (Sweden)

    H. V. Lee

    2014-01-01

    Full Text Available Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate’s application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein.

  3. Structural simplification of chemical reaction networks in partial steady states.

    Science.gov (United States)

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology.

  4. Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications.

    Science.gov (United States)

    Li-Beisson, Yonghua; Nakamura, Yuki; Harwood, John

    2016-01-01

    Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

  5. The Physical and Chemical Structure of Hot Molecular Cores

    CERN Document Server

    Nomura, H

    2004-01-01

    We have made self-consistent models of the density and temperature profiles of the gas and dust surrounding embedded luminous objects using a detailed radiative transfer model together with observations of the spectral energy distribution of hot molecular cores. Using these profiles we have investigated the hot core chemistry which results when grain mantles are evaporated, taking into account the different binding energies of the mantle molecules, as well a model in which we assume that all molecules are embedded in water ice and have a common binding energy. We find that most of the resulting column densities are consistent with those observed toward the hot core G34.3+0.15 at a time around 10$^4$ years after central luminous star formation. We have also investigated the dependence of the chemical structure on the density profile which suggests an observational possibility of constraining density profiles from determination of the source sizes of line emission from desorbed molecules.

  6. Lincosamides: Chemical structure, biosynthesis, mechanism of action, resistance, and applications.

    Science.gov (United States)

    Spížek, Jaroslav; Řezanka, Tomáš

    2017-06-01

    Lincomycin and its derivatives are antibiotics exhibiting biological activity against bacteria, especially Gram-positive ones, and also protozoans. Lincomycin and its semi-synthetic chlorinated derivative clindamycin are widely used in clinical practice. Both antibiotics are bacteriostatic, inhibiting protein synthesis in sensitive bacteria; however, at higher concentrations, they may be bactericidal. Clindamycin is usually much more active than lincomycin in the treatment of bacterial infections, in particular those caused by anaerobic species; it can also be used for the treatment of important protozoal diseases, e.g. malaria, most effectively in combination with other antibiotic or non-antibiotic antimicrobials (primaquine, fosfidomycin, benzoyl peroxide). Chemical structures of lincosamide antibiotics and the biosynthesis of lincomycin and its genetic control have been summarized and described. Resistance to lincomycin and clindamycin may be caused by methylation of 23S ribosomal RNA, modification of the antibiotics by specific enzymes or active efflux from the bacterial cell. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Pigments of Staphylococcus aureus, a series of triterpenoid carotenoids.

    Science.gov (United States)

    Marshall, J H; Wilmoth, G J

    1981-01-01

    The pigments of Staphylococcus aureus were isolated and purified, and their chemical structures were determined. All of the 17 compounds identified were triterpenoid carotenoids possessing a C30 chain instead of the C40 carotenoid structure found in most other organisms. The main pigment, staphyloxanthin, was shown to be alpha-D-glucopyranosyl 1-O-(4,4'-diaponeurosporen-4-oate) 6-O-(12-methyltetradecanoate), in which glucose is esterified with both a triterpenoid carotenoid carboxylic acid and a C15 fatty acid. It is accompanied by isomers containing other hexoses and homologs containing C17 fatty acids. The carotenes 4,4'-diapophytoene, 4,4'-diapophytofluene, 4-4'-diapophytofluene, 4-4'-diapo-zeta-carotene, 4,4'-diapo-7,8,11,12-tetrahydrolycopene, and 4,4'-diaponeurosporene and the xanthophylls 4,4'-diaponeurosporenal, 4,4'-diaponeurosporenoic acid, and glucosyl diaponeurosporenoate were also identified, together with some of their isomers or breakdown products. The symmetrical 4,4'-diapo- structure was adopted for these triterpenoid carotenoids, but an alternative unsymmetrical 8'-apo-structure could not be excluded. PMID:7275936

  8. Structural and Optical Study of Chemical Bath Deposited Nano-Structured CdS Thin Films

    Science.gov (United States)

    Kumar, Suresh; Sharma, Dheeraj; Sharma, Pankaj; Sharma, Vineet; Barman, P. B.; Katyal, S. C.

    2011-12-01

    CdS is commonly used as window layer in polycrystalline solar cells. The paper presents a structural and optical study of CdS nano-structured thin films. High quality CdS thin films are grown on commercial glass by means of chemical bath deposition. It involves an alkaline solution of cadmium salt, a complexant, a chalcogen source and a non-ionic surfactant. The films have been prepared under various process parameters. The chemically deposited films are annealed to estimate its effect on the structural and optical properties of films. These films (as -deposited and annealed) have been characterized by means of XRD, SEM and UV-Visible spectrophotometer. XRD of films show the nano-crystalline nature. The energy gap of films is found to be of direct in nature.

  9. Identification of structure-activity relationships from screening a structurally compact DNA-encoded chemical library.

    Science.gov (United States)

    Franzini, Raphael M; Ekblad, Torun; Zhong, Nan; Wichert, Moreno; Decurtins, Willy; Nauer, Angela; Zimmermann, Mauro; Samain, Florent; Scheuermann, Jörg; Brown, Peter J; Hall, Jonathan; Gräslund, Susanne; Schüler, Herwig; Neri, Dario

    2015-03-23

    Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA-encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL-100K, a DNA-encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA-sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate-specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small-molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Filamentous fungi are large-scale producers of pigments and colorants for the food industry.

    Science.gov (United States)

    Dufossé, Laurent; Fouillaud, Mireille; Caro, Yanis; Mapari, Sameer A S; Sutthiwong, Nuthathai

    2014-04-01

    With globalization in the research trends, healthier life styles, and the growing market for the natural food colorants in the economically fast-growing countries all over the world, filamentous fungi are being investigated as readily available sources of chemically diverse colorants. With two selected examples, polyketide-Monascus-like pigments from the new fungal production strains, and the promising and yet unexplored hydroxy-anthraquinoid colorants, the present review highlights exciting recent findings, which may pave the way for alternative and/or additional biotechnological processes for the industrial production of natural food colorants of improved functionality. As an additional aspect, marine fungi are discussed as potential sources of novel pigments of numerous color hues and atypical chemical structures.

  11. Microglia in the mouse retina alter the structure and function of retinal pigmented epithelial cells: a potential cellular interaction relevant to AMD.

    Directory of Open Access Journals (Sweden)

    Wenxin Ma

    Full Text Available BACKGROUND: Age-related macular degeneration (AMD is a leading cause of legal blindness in the elderly in the industrialized word. While the immune system in the retina is likely to be important in AMD pathogenesis, the cell biology underlying the disease is incompletely understood. Clinical and basic science studies have implicated alterations in the retinal pigment epithelium (RPE layer as a locus of early change. Also, retinal microglia, the resident immune cells of the retina, have been observed to translocate from their normal position in the inner retina to accumulate in the subretinal space close to the RPE layer in AMD eyes and in animal models of AMD. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we examined the effects of retinal microglia on RPE cells using 1 an in vitro model where activated retinal microglia are co-cultured with primary RPE cells, and 2 an in vivo mouse model where retinal microglia are transplanted into the subretinal space. We found that retinal microglia induced in RPE cells 1 changes in RPE structure and distribution, 2 increased expression and secretion of pro-inflammatory, chemotactic, and pro-angiogenic molecules, and 3 increased extent of in vivo choroidal neovascularization in the subretinal space. CONCLUSIONS/SIGNIFICANCE: These findings share similarities with important pathological features found in AMD and suggest the relevance of microglia-RPE interactions in AMD pathogenesis. We speculate that the migration of retinal microglia into the subretinal space in early stages of the disease induces significant changes in RPE cells that perpetuate further microglial accumulation, increase inflammation in the outer retina, and fosters an environment conducive for the formation of neovascular changes responsible for much of vision loss in advanced AMD.

  12. Using invertebrate remains and pigments in the sediment to infer changes in trophic structure after fish introduction in Lake Fogo: a crater lake in the Azores

    DEFF Research Database (Denmark)

    Skov, Tue; Buchaca, Teresa; Amsinck, Susanne Lildal

    2010-01-01

    to a pelagic dominated ecosystem, as cryptophytes became markedly more abundant at the expense of benthic diatoms. Trout introduction was followed by a return to a more benthic cladoceran and benthic algae (pigments) dominated state, which we attribute to trout predation on carp leading to improved water......Fish introduction may have marked effects on the trophic dynamics and ecological state of former fishless lakes, but due to scarcity of historical data this can seldom be documented. We used remains of cladoceran, chironomid and pigment assemblages in the sediment archive to unravel the effect...

  13. Laugier-hunziker pigmentation

    Directory of Open Access Journals (Sweden)

    Ajith C

    2005-01-01

    Full Text Available Laugier-Hunziker pigmentation (LHP is an acquired disorder of hypermelanosis characterized by mucocutaneous hyperpigmentation. LHP may resemble various disorders characterized by mucocutaneous pigmentation. A 58-year-old lady presented with progressively increasing number of variable sized, hyperpigmented macules over the lips, fingers, toes and nails. There was no family history of similar illness. Systemic examination and all relevant investigations were within normal limits. Histopathology of a skin lesion had features consistent with LHP. The diagnosis of LHP must be made only after relevant investigations to rule out any associated systemic involvement. This case further highlights that LHP is not restricted to European countries.

  14. Phytoplankton community structure and stocks in the Southern Ocean (30-80°E) determined by CHEMTAX analysis of HPLC pigment signatures

    Science.gov (United States)

    Wright, Simon W.; van den Enden, Rick L.; Pearce, Imojen; Davidson, Andrew T.; Scott, Fiona J.; Westwood, Karen J.

    2010-05-01

    southward following the retreating sea ice. We suggest that grazing of the bloom and export of faecal pellets stripped the upper water column of iron (as suggested by low Fv/Fm ratios and CHEMTAX pigment ratios in Haptophytes - iron was not measured). Thus, export of iron by grazing, and possibly sedimentation, created a southward migrating iron gradient, limiting growth in the upper water column. North of the postulated iron gradient, a nanoflagellate community developed at depth, with Chl a stocks from 36-49 mg m -2. This community was probably based on regenerated production, sustained by residual and/or upwelling iron, as indicated by a close correspondence between distributions of Chl a and profiles of Fv/Fm. The community consisted of haptophytes (chiefly Phaeocystis gametes), dinoflagellates, prasinophytes, cryptophytes, and some small diatoms. Selective grazing by krill may have fashioned and maintained the community. North of the SB, Chl a ranged from 40-67 mg m -2 and was found predominantly in the mixed layer, but Fv/Fm ratios remained low, suggesting the community of P. antarctica and diatoms was iron-limited. These interpretations provide a cogent explanation for the composition and structure of late summer microbial populations in the marginal ice zone.

  15. Dihydrolindbladiones, three new naphthoquinone pigments from a myxomycete Lindbladia tubulina.

    Science.gov (United States)

    Misono, Yuka; Ishikawa, Yae; Yamamoto, Yukinori; Hayashi, Masahiko; Komiyama, Kanki; Ishibashi, Masami

    2003-07-01

    Three new naphthoquinone pigments, 6,7-dimethoxydihydrolindbladione (1), dihydrolindbladione (2), and 6-methoxydihydrolindbladione (3), have been isolated from a myxomycete Lindbladia tubulina, and their structures were elucidated by spectral data. Compound 3 appreciably exhibited a reversal effect of multidrug resistance. Lindbladione (4), the major pigment of this myxomycete, was also isolated from Cribraria intricata.

  16. Raman spectroscopy of modern art: classification and identification of Azo-pigments

    Science.gov (United States)

    Vandenabeele, Peter; Moens, Luc; Edwards, Howell G.

    2000-09-01

    Micro-Raman spectroscopy is an important molecular spectroscopic technique for the non-destructive examination of objects of art. In this work, Raman spectra of a number of Azo-pigments are presented, which are important artists' pigments in contemporary artifacts. The Azo-pigments, being a group of cheap pigments with good painting properties, form an important subgroup of pigments that became available to the artists at the end of the 19th and the beginning of the 20th century. A classification for these Azo-pigments is presented, which is based on their chemical properties, reflected in their molecular Raman spectrum. It is shown that a close spectral examination can help in assigning the unknown pigment to a class of pigments and thus assist in the identification of the painting material.

  17. True bursal pigmented villonodular synovitis

    Energy Technology Data Exchange (ETDEWEB)

    Abdelwahab, Ibrahim Fikry [Department of Radiology, New York Methodist Hospital, Affiliated with New York Hospital-Cornell Medical Center, Brooklyn, NY (United States); Kenan, Samuel [Department of Orthopedics, New York University Medical Center, NY (United States); Steiner, German C. [Department of Pathology, Hospital for Joint Diseases/Orthopedic Institute, New York, NY (United States); Abdul-Quader, Mohammed [Department of Radiology, New York Presbyterian Hospital, Columbia University, New York, NY (United States)

    2002-06-01

    We describe two cases of pigmented villonodular synovitis affecting true bursae. This study was also designed to discuss the term ''pigmented villonodular bursitis'', not confined to true synovial bursae, sometimes creating misunderstanding. (orig.)

  18. Raman af hvide pigmenter

    DEFF Research Database (Denmark)

    Reeler, Nini Elisabeth Abildgaard; Nielsen, Ole Faurskov; Sauer, Stephan P. A.;

    2013-01-01

    Et samspil mellem kunst og kemi. I et samarbejde mellem Statens Museum for Kunst og Kemisk Institut på KU er Ramanspek-troskopi brugt til at definere sammensætningen af blandinger af blyhvidt og calcit i maleriers hvide pigmenter....

  19. Pigmented villonodular synovitis

    Energy Technology Data Exchange (ETDEWEB)

    Al-Nakshabandi, N.A.; Ryan, A.G.; Choudur, H.; Torreggiani, W.; Nicoloau, S.; Munk, P.L. E-mail: plmunk@interchange.ubc.ca; Al-Ismail, K

    2004-05-01

    Pigmented villonodular synovitis (PVNS) is a rare benign proliferative growth of the synovium of obscure aetiology with a wide spectrum of clinical presentations and imaging findings. The purpose of this review is to acquaint the reader with the spectrum of imaging features of PVNS using a variety of imaging techniques.

  20. Using of cyanobacteria pigments

    OpenAIRE

    Кардаш, О. В.; Національний авіаційний університет; Курейшевич, А. В.; Інститут гідробіології НАН України; Васильченко, О. А.; Національний авіаційний університет

    2012-01-01

    Photosynthetic apparatus of all organisms contains light absorbing pigments. Cyanobacteria pigments may be divided into three groups – chlorophylls, carotenoids and phycobiliproteins. Pigments may be used in the food and pharmaceutical industry. Cyanobacteria pigments features and usage possibilities are observed. Фотосинтезирующий аппарат всех организмов состоит из поглощающих свет пигментов. Пигменты цианобактерий можно разделить на три группы – хлорофиллы, каротиноиды и фикобилипротеины...

  1. Raman af hvide pigmenter

    DEFF Research Database (Denmark)

    Reeler, Nini Elisabeth Abildgaard; Nielsen, Ole Faurskov; Sauer, Stephan P. A.

    2013-01-01

    Et samspil mellem kunst og kemi. I et samarbejde mellem Statens Museum for Kunst og Kemisk Institut på KU er Ramanspek-troskopi brugt til at definere sammensætningen af blandinger af blyhvidt og calcit i maleriers hvide pigmenter....

  2. Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

    Science.gov (United States)

    Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

    2012-01-01

    Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

  3. Chemical etching of deformation sub-structures in quartz

    Science.gov (United States)

    Wegner, M. W.; Christie, J. M.

    1983-02-01

    Chemical etching of dislocations has been studied in natural and synthetic quartz single crystals, in deformed synthetic quartz and in naturally and experimentally deformed quartzites. The ability of different etchants to produce polished or preferentially etched surfaces on quartz is described. Dislocation etching was achieved on all crystal planes examined by using a saturated solution of ammonium bifluoride as the etchant. Appropriate etching times were determined for etching quartzites for grain size, subgrain boundaries, deformation lamellae, dislocations and twins. Growth and polished surfaces of synthetic single crystal quartz were similarly etched and dislocation etch pits, characteristic of various orientations were found. The use of ammonium bifluoride proved to be expecially advantageous for the basal plane, producing a polished surface with etch pits, suitable for dislocation etch pit counting. “Double” etch pits have been found on Dauphiné twin boundaries on the basal plane and the first order prism, using this etchant. Slip lines and deformation bands were suitably etched on deformed synthetic crystal surfaces for identification of the slip planes. Other acidic etchants have been explored and their application to the study of deformation structures in quartz crystals is discussed.

  4. Nepheline structural and chemical dependence on melt composition

    Energy Technology Data Exchange (ETDEWEB)

    Marcial, José; Crum, Jarrod; Neill, Owen; McCloy, John

    2016-02-01

    Nepheline crystallizes upon slow-cooling in some melts concentrated in Na2O and Al2O3, which can result in a residual glass phase of low chemical durability. Nepheline can incorporate many components often found in high-level waste radioactive borosilicate glass, including glass network ions (e.g., Si, Al, Fe), alkali metals (e.g., Cs, K, Na, and possibly Li), alkaline-earth metals (e.g., Ba, Sr, Ca, Mg), and transition metals (e.g., Mn, and possibly Cr, Zn, Ni). When crystallized from melts of different compositions, nepheline chemistry varies as a function of starting glass composition. Five simulated high level nuclear waste borosilicate glasses shown to crystallize large fractions of nepheline on slow cooling, were selected for study. These melts constituted a range of Al2O3, B2O3, CaO, Na2O, K2O, Fe2O3, and SiO2 compositions. Compositional analyses of nepheline crystals in glass by electron probe micro-analysis (EPMA) indicate that boron is unlikely to be present in any significant concentration, if at all, in nepheline. Also, several models are presented for calculating the fraction of vacancies in the nepheline structure.

  5. STRUCTURE AND CHARACTERIZATION OF SOME HIGH CHEMICALLY RESISTANCE SILICATE GLASSES

    Directory of Open Access Journals (Sweden)

    H.A. Abo-Mosallam

    2016-10-01

    Full Text Available A multi component silicate glasses based on Li₂O-MgO-P₂O₅-SiO₂ system were synthesized and modified by Na₂O /Li₂O, SrO /MgO and CaO /SrO replacements. The prepared glasses have been characterized by X-ray Diffraction (XRD and Fourier Transform Infrared Spectroscopy (FTIR. Additionally, bulk density, microhardness, chemical durability and in vitro bioactivity were evaluated as a function of introducing different alkali and alkaline element substitutions. For comprehension the in vitro bioactivity, the glass samples were soaking in simulated body fluid (SBF solution at 37°C for 14 days. Scanning electron microscopy coupled with energy-dispersive X-ray (SEM-EDX and (FTIR were used to characterize forming hydroxyapatite layer produced on glass specimen surfaces. The results show that Na₂O/Li₂O and CaO/SrO replacements led to enhance the bioactivity behavior of the glasses. The results are harmonious with a weaker network glass structure consequence of Na₂O/Li₂O and SrO/MgO replacement in the glasses. However, the glass network connectivity increased with addition of the higher charge to size ratio of Ca2+ instead of Sr2+. The prepared glass samples had microhardness in the range, 4920-6017 MPa; density values in the range, 2.46-2.78 g/cm³ and the weight loss percent was ranged between 0.72 and 1.67 %.

  6. Phototrophic pigment production with microalgae

    NARCIS (Netherlands)

    Mulders, K.J.M.

    2014-01-01

    Abstract

    Microalgal pigments are regarded as natural alternatives for food colorants. To facilitate optimization of microalgae-based pigment production, this thesis aimed to obtain key insights in the pigment metabolism of phototrophic microalgae, with the main  focus

  7. Phototrophic pigment production with microalgae

    NARCIS (Netherlands)

    Mulders, K.J.M.

    2014-01-01

    Abstract

    Microalgal pigments are regarded as natural alternatives for food colorants. To facilitate optimization of microalgae-based pigment production, this thesis aimed to obtain key insights in the pigment metabolism of phototrophic microalgae, with the main  focus

  8. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    Energy Technology Data Exchange (ETDEWEB)

    Sadtler, Bryce F [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2009-05-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or

  9. Detection of Pigment Networks in Dermoscopy Images

    Science.gov (United States)

    Eltayef, Khalid; Li, Yongmin; Liu, Xiaohui

    2017-02-01

    One of the most important structures in dermoscopy images is the pigment network, which is also one of the most challenging and fundamental task for dermatologists in early detection of melanoma. This paper presents an automatic system to detect pigment network from dermoscopy images. The design of the proposed algorithm consists of four stages. First, a pre-processing algorithm is carried out in order to remove the noise and improve the quality of the image. Second, a bank of directional filters and morphological connected component analysis are applied to detect the pigment networks. Third, features are extracted from the detected image, which can be used in the subsequent stage. Fourth, the classification process is performed by applying feed-forward neural network, in order to classify the region as either normal or abnormal skin. The method was tested on a dataset of 200 dermoscopy images from Hospital Pedro Hispano (Matosinhos), and better results were produced compared to previous studies.

  10. Production of a Blue Pigment (Glaukothalin) by Marine Rheinheimera spp.

    OpenAIRE

    Hans-Peter Grossart; Marc Thorwest; Inken Plitzko; Thorsten Brinkhoff; Meinhard Simon; Axel Zeeck

    2009-01-01

    Two γ-Proteobacteria strains, that is, HP1 and HP9, which both produce a diffusible deep blue pigment, were isolated from the German Wadden Sea and from the Øresund, Denmark, respectively. Both strains affiliate with the genus Rheinheimera. Small amounts of the pigment could be extracted from HP1 grown in a 50 L fermenter and were purified chromatographically. Chemical analysis of the pigment including NMR and mass spectrometry led to a molecular formula of C34H56N4O4 (m.w. 584.85) which has ...

  11. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile

    Science.gov (United States)

    Arjunan, V.; Thillai Govindaraja, S.; Jose, Sujin P.; Mohan, S.

    2014-07-01

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G**, high level 6-311++G** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.

  12. Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

    Science.gov (United States)

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  13. Determination of pigments in vegetables.

    Science.gov (United States)

    Schoefs, Benoît

    2004-10-29

    Plant pigments are responsible for the shining color of plant tissues. They are also found in animal tissues and, eventually in transformed food products as additives. These pigments have an important impact on the commercial value of products, because the colors establish the first contact with the consumer. In addition plant pigments may have an influence on the health of the consumers. Pigments are labile: they can be easily altered, and even destroyed. Analytical processes have been developed to determine pigment composition. The aim of this paper is to provide a brief overview of these methods.

  14. Integrating Epistemological Perspectives on Chemistry in Chemical Education: The Cases of Concept Duality, Chemical Language, and Structural Explanations

    Science.gov (United States)

    Kaya, Ebru; Erduran, Sibel

    2013-07-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ( Foundations of Chemistry 1:225-238, 1999) notion of concept duality, Jacob's ( HYLE-International Journal for Philosophy of Chemistry 7:31-50, 2001) descriptions of chemical language and Goodwin's ( Foundations of Chemistry 10:117-127, 2008) explication of structural explanations in organic chemistry to highlight the particular ways in which chemical knowledge is structured. We use examples of textbooks and curricula to illustrate that even though the mentioned aspects of are relevant to and are covered in educational contexts, the philosophical dimensions of this coverage is absent in textbooks and curricula. The emphasis in the use of these features of chemical knowledge seems to be more on the conceptual definitions rather than on their "epistemological nature". We argue that chemical education will be improved through the inclusion of the philosophical perspectives in chemistry teaching and learning by highlighting the specific ways in which chemical knowledge functions.

  15. Protein structure refinement using a quantum mechanics-based chemical shielding predictor

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Jensen, Jan Halborg

    2017-01-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...

  16. Structure and functions of fungal cell surfaces

    Science.gov (United States)

    Nozawa, Y.

    1984-01-01

    A review with 24 references on the biochemistry, molecular structure, and function of cell surfaces of fungi, especially dermatophytes: the chemistry and structure of the cell wall, the effect of polyene antibiotics on the morphology and function of cytoplasmic membranes, and the chemical structure and function of pigments produced by various fungi are discussed.

  17. Pigmentos maculares Macular pigments

    Directory of Open Access Journals (Sweden)

    Renata Canovas

    2009-12-01

    Full Text Available A luteína e a zeaxantina são pigmentos amarelos que se localizam na mácula. Devido à sua localização, diminuem e filtram a quantidade de luz principalmente azul que chega aos fotorreceptores, atuam como antioxidantes e podem melhorar a qualidade visual. Esta é uma revisão do seu mecanismo de incorporação, ação, possíveis aplicações e conhecimento científico a respeito.Lutein and Zeaxanthin are yellow pigments located at the macula. Because of your location macular pigments decrease and filter the amount of blue light that reach photoreceptors, protect the outer retina from oxidative stress and may improve the vision quality. This is a review regarding incorporation mechanism, function and knowledge update.

  18. Characterization of Electrochemical and Morphological Properties of Iron-Phosphate-Silicate Chemical Garden Structures

    Science.gov (United States)

    Doloboff, I. J.; Barge, L. M.; Russell, M. J.; Kanik, I.

    2012-03-01

    Examination of the growth of Fe^2^+, phosphate, and silicate chemical garden structures to understand properties of similar structures that may have formed at Hadean alkaline hydrothermal vents which may play an important role in the emergence of life.

  19. The photochromic effect of bismuth vanadate pigments. Part I: Synthesis, characterization and lightfastness of pigment coatings

    Science.gov (United States)

    Tücks, A.; Beck, H. P.

    2005-04-01

    We report on investigations of the photochromic effect of BiVO 4 pigments. Emphasis is placed on an approach widely used in industrial color testing. By means of colorimetry Δ E ab*-values, which measure the perceived color difference, can be calculated from reflectance spectra of non-illuminated and illuminated pigment coatings. Pigments were prepared by either wet-chemical precipitation or solid-state reactions. Depending on the choice of starting compounds, lightfastness was found to vary significantly. Small amounts of impurity phases do not seem to affect photochromism. In contrast, impurities like Fe and Pb cause intense photochromism. The role of Fe is suggested by trace analyses, which (in case of pigments synthesized by precipitation reactions) reveal a correlation between concentration and Δ E ab*. Indications are found that other effects like pigment-lacquer interactions might also be of importance. Difference reflectance spectra turn out to vary in shape depending on the type and concentration of impurities or dopants. For BiVO 4 at least three different mechanisms of photochromism can be assumed.

  20. Pigment dispersion syndrome

    Directory of Open Access Journals (Sweden)

    C.S. Sandhya

    2013-10-01

    Full Text Available We report of the rare occurrence of pigment dispersion syndrome (PDS with posterior subcapsular cataract in both eyes in a young male patient. The patient presented with complaints of progressive decrease in vision of one year duration. The patient also had high myopia with mild iridodonesis, phacodonesis and anterior insertion of zonules. Classical signs of PDS like Krukenberg's spindle on the posterior corneal surface were evident on slit lamp examination; transillumination defects in the iris could not be elicited by retroillumination as the iris was heavily pigmented. Gonioscopy revealed heavy and uniform pigmentation of trabecular meshwork. Evidence of a characteristic iris configuration on optical coherence tomography (OCT, namely, posterior bowing of iris in the mid periphery suggested the diagnosis of PDS. This case highlights the importance of OCT in identifying the iris configuration characteristically seen in PDS even in the absence of transillumination defects in the iris and reiterates the need to look for subtle signs like phacodonesis which are important when surgical intervention is planned.

  1. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    OpenAIRE

    Sadtler, Bryce F

    2010-01-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions of a nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size an...

  2. A probabilistic model for secondary structure prediction from protein chemical shifts.

    Science.gov (United States)

    Mechelke, Martin; Habeck, Michael

    2013-06-01

    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts.

  3. Optical and structural properties of multi-wall-carbonnanotube-modified ZnO synthesized at varying substrate temperatures for highly efficient light sensing devices

    CSIR Research Space (South Africa)

    Saasa, V

    2015-12-01

    Full Text Available Melanins are difficult to characterize because of their intractable chemical properties and the heterogeneity in their structural features. Melanin pigments, in fact, are composed of many different types of monomeric units that are connected through...

  4. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  5. Contemporary artists' spinel pigments: Non-invasive characterization by means of electronic spectroscopy

    Science.gov (United States)

    Angelin, Eva Mariasole; Bacci, Mauro; Bartolozzi, Giovanni; Cantisani, Emma; Picollo, Marcello

    2017-02-01

    The identification of artistic materials represents a fundamental step in supporting the conservation of cultural heritage objects. The importance of their appropriate characterization is particularly relevant in modern-contemporary art, since they could be affected by the occurrence of rapid changes in chemical formulation over time. This paper focuses on an investigation of a series of contemporary blue-green commercial acrylic paints constituted of spinel pigments, using non-invasive spectroscopic techniques. The spectroscopic and color measurements obtained make it possible to characterize the acrylic paints under investigation and to compare the results obtained with those reported in the literature and in spectral databases. To be more precise, the proposed UV-vis-NIR reflectance spectroscopic technique was sensitive enough to characterize the acrylic paints according to their d-d ligand field and the charge transfer (CT) electronic transitions involved in the spinel structures. In addition, an overview of this class of inorganic pigments is also given.

  6. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    Science.gov (United States)

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.

  7. 75 FR 13257 - Carbazole Violet Pigment 23 from India: Final Results of the Expedited Five-year (Sunset) Review...

    Science.gov (United States)

    2010-03-19

    ... interested parties and Petitioners in the original investigation, Nation Ford Chemical Company and Sun... Color Index No. 51319 and Chemical Abstract No. 6358-30-1, with the chemical name of diindolo... the form of presscake and dry color. Pigment dispersions in any form (e.g., pigments dispersed...

  8. Structural characterization and stability of antibacterial pigment from Pseudomonas aeruginosa%铜绿假单胞菌抗菌色素的结构鉴定及稳定性检测

    Institute of Scientific and Technical Information of China (English)

    谯天敏; 张静; 赵芳; 朱天辉

    2015-01-01

    The antagonistic substance of Pseudomonas aeruginosa can effectively antagonize Arthrinium phaeospermum (Corda)M.B.Elli. The yellow oily substances with strong microbe-inhibiting activity were included through silica gel col?umn chromatography and UV elution after pretreatment of the filtrate of fermentation broth adopting trichloromethane ex?traction. By nuclear magnetic resonance and infrared spectrum detection, the compound was proved a phenazine pigment with aromatic rings, and with the chemical formula C14 H10 O2 N2 . Furthermore, the pigment stability test showed that illu?mination and temperature exerted slight effects on pigment activity. Light concentrate oxidizer and reducing agent exerted small effects on it, while the heavy concentrate was on contrary. The pigment activity was up to its max when pH was 7-8; when pH≤3, it was instability and almost with no bacteriostatic activity. Metallic ion could affect the pigment stabili?ty in varying degrees, Na+,K+,Ba2+,Ca2+ and Ag+ exerted a light effect on pigment' s stability, however, Al3+,Cu2+, Fe3+,Pb2+ exerted a heavy influence, which nearly caused it lost all activities.%铜绿假单胞菌( Pseudomonas aeruginosa)产生的拮抗物质对撑×绿杂交竹梢枯病病原菌具有明显的抑制作用. 铜绿假单胞菌发酵液预处理后,采用三氯甲烷萃取得到活性粗提物,后经硅胶柱色谱分离及紫外洗脱检测,得到抑菌活性最强的黄色油状活性物质. 经核磁共振和红外光谱检测,得出该活性物质是一种有芳香环的吩嗪类化合物,化学式为C14 H10 O2 N2. 色素稳定性的研究表明,光照、温度对活性色素的稳定性影响甚微;低浓度的氧化剂和还原剂对活性色素的稳定性影响较小,高浓度对其影响较大;色素在偏中性或碱性条件下( pH7~8)活性最大,当pH≤3时,色素性质不稳定,抑菌活性几近消失;金属离子对色素稳定性有不同程度的影响,其中Na+、K+、Ba2+、Ca2+、Ag

  9. Anthocyanins. Plant pigments and beyond.

    Science.gov (United States)

    Santos-Buelga, Celestino; Mateus, Nuno; De Freitas, Victor

    2014-07-23

    Anthocyanins are plant pigments widespread in nature. They play relevant roles in plant propagation and ecophysiology and plant defense mechanisms and are responsible for the color of fruits and vegetables. A large number of novel anthocyanin structures have been identified, including new families such as pyranoanthocyanins or anthocyanin oligomers; their biosynthesis pathways have been elucidated, and new plants with "a la carte" colors have been created by genetic engineering. Furthermore, evidence about their benefits in human health has accumulated, and processes of anthocyanin absorption and biotransformation in the human organism have started to be ascertained. These advances in anthocyanin research were revised in the Seventh International Workshop on Anthocyanins that took place in Porto (Portugal) on September 9-11, 2013. Some selected papers are collected in this special issue, where aspects such as anthocyanin accumulation in plants, relationship with color expression, stability in plants and food, and bioavailability or biological activity are revised.

  10. Nonphotosynthetic Pigments as Potential Biosignatures

    CERN Document Server

    Schwieterman, Edward W; Meadows, Victoria S

    2015-01-01

    Previous work on possible surface reflectance biosignatures for Earth-like planets has typically focused on analogues to spectral features produced by photosynthetic organisms on Earth, such as the vegetation red edge. Although oxygenic photosynthesis, facilitated by pigments evolved to capture photons, is the dominant metabolism on our planet, pigmentation has evolved for multiple purposes to adapt organisms to their environment. We present an interdisciplinary study of the diversity and detectability of nonphotosynthetic pigments as biosignatures, which includes a description of environments that host nonphotosynthetic biologically pigmented surfaces, and a lab-based experimental analysis of the spectral and broadband color diversity of pigmented organisms on Earth. We test the utility of broadband color to distinguish between Earth-like planets with significant coverage of nonphotosynthetic pigments and those with photosynthetic or nonbiological surfaces, using both 1-D and 3-D spectral models. We demonstr...

  11. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  12. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  13. Branch Structure of Corona Discharge:Experimental Simulation and Chemical Properties

    Institute of Scientific and Technical Information of China (English)

    邹吉军; 刘昌俊

    2004-01-01

    The branch structure of corona discharge has been investigated via C2H2 corona discharge. Carbon filament with excellent branch structure is formed in the discharge. This carbon filament offers a direct mimic of the branch structure of corona discharge. It providesa very useful way to study on the average energy, physical and chemical characteristics of coronadischarge. On this basis, the chemical property of corona discharge for methane conversion is discussed.

  14. Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

    Science.gov (United States)

    Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

    2008-06-01

    A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

  15. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  16. 黄海胆棘壳色素理化性质和稳定性的研究%Physico-chemical Properties and Stability of Pigments from Spine and Shell of Sea Urchin Glyptocidaris crenularis

    Institute of Scientific and Technical Information of China (English)

    王晓东; 周大勇; 朱蓓薇; 吕艳红

    2012-01-01

    对黄海胆棘壳色素理化性质及稳定性进行研究。结果表明:黄海胆棘壳色素在水、甲醇等极性溶剂中溶解性较好,在石油醚、正己烷等非极性溶剂中溶解性较差;在酸性环境中显橘黄色,在碱性环境中显土黄色;耐热性较好,但耐光性较差;Na2SO3和山梨酸钾既可引起色素颜色改变,又可降低色素稳定性;H2O2和NaCl不改变色素颜色,但可降低色素稳定性;高质量浓度蔗糖可增强色素稳定性;VC对色素起到护色增色作用。%The present study aimed to characterize physicochemical properties and stability of pigments extracted from the spine and shell of sea urchin(Glyptocidaris crenularis).Our results showed that the pigments had relatively high solubility in polar solvents such as water and methanol but had relatively low solubility in non-polar solvents such as light petroleum and hexane.The pigments showed orange color in acidic conditions but yellowish brown color in basic conditions.The pigments were relatively stable to heat but unstable to light.Na2SO3 and potassium sorbate could not only cause changes in the color but also decrease the stability of the pigments.H2O2 and NaCl could not cause any changes in the color but decrease the stability of the pigments.High concentrations of cane sugar could enhance the stability of the pigments.Vitamin C could protect and enhance the color of the pigments.

  17. Effects of chemical treatments on hemp fibre structure

    Energy Technology Data Exchange (ETDEWEB)

    Kabir, M.M., E-mail: kabirm@usq.edu.au [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Wang, H. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Lau, K.T. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia); Department of Mechanical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region (Hong Kong); Cardona, F. [Centre of Excellence in Engineered Fibre Composite (CEEFC), Faculty of Engineering and Surveying, University of Southern Queensland, Toowoomba, Queensland 4350 (Australia)

    2013-07-01

    In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

  18. Tabletop imaging of structural evolutions in chemical reactions

    CERN Document Server

    Ibrahim, Heide; Beaulieu, Samuel; Schmidt, Bruno E; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Sanderson, Joseph; Schuurman, Michael S; Légaré, François

    2014-01-01

    The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using VUV light from a Free Electron Laser [Phys. Rev. Lett. 105, 263002 (2010)]. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond-breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and definitively quantitative ab initio trajectory simulations.

  19. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    Energy Technology Data Exchange (ETDEWEB)

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  20. Mining the chemical quarry with joint chemical probes: an application of latent semantic structure indexing (LaSSI) and TOPOSIM (Dice) to chemical database mining.

    Science.gov (United States)

    Singh, S B; Sheridan, R P; Fluder, E M; Hull, R D

    2001-05-10

    In this study we use a novel similarity search technique called latent semantic structure indexing (LaSSI) with joint chemical probes as queries to mine the MDL drug data report database. LaSSI is based on latent semantic indexing developed for searching textual databases. We use atom pair and topological torsion descriptors in our calculations. The results obtained with LaSSI are compared with another in-house similarity search technique TOPOSIM. The results from the similarity searches using joint chemical probes are significantly better than searches using single chemical probes for both LaSSI and TOPOSIM. The selected molecules are closely related in activity to their queries and are ranked among the top 300 scoring molecules of the 82 860 entries in the database. Our implementation of LaSSI is very fast and efficient in finding active compounds. The results also show that LaSSI consistently retrieves more diverse chemical structures representative of the joint chemical probes in comparison to TOPOSIM. The use of multimolecule topological probes to identify compounds complements the use of searching databases with 3D pharmacophore hypotheses.

  1. Electronic and chemical properties of graphene-based structures:

    DEFF Research Database (Denmark)

    Vanin, Marco

    In the present thesis several aspects of graphene-based structures have been investigated using density functional theory calculations to solve the electronic structure problem. A review of the implementation of a localized basis-set within the projector augmented wave method - the way of describ...... are attractive candidates although issues regarding the poisoning of the active site remain to be addressed....

  2. Chemical Tagging Can Work: Identification of Stellar Phase-space Structures Purely by Chemical-abundance Similarity

    Science.gov (United States)

    Hogg, David W.; Casey, Andrew R.; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel; Hasselquist, Sten; Ho, Anna Y. Q.; Holtzman, Jon A.; Majewski, Steven R.; Martell, Sarah L.; Mészáros, Szabolcs; Nidever, David L.; Shetrone, Matthew

    2016-12-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were, in fact, born together (in the same molecular cloud) long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ∼ {10}5 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space, and we recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at the survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon the prospects for future data sets appear very good.

  3. Origin of the exotic blue color of copper-containing historical pigments.

    Science.gov (United States)

    García-Fernández, Pablo; Moreno, Miguel; Aramburu, José Antonio

    2015-01-05

    The study of chemical factors that influence pigment coloring is a field of fundamental interest that is still dominated by many uncertainties. In this Article, we investigate, by means of ab initio calculations, the origin of the unusual bright blue color displayed by historical Egyptian Blue (CaCuSi4O10) and Han Blue (BaCuSi4O10) pigments that is surprisingly not found in other compounds like BaCuSi2O6 or CaCuO2 containing the same CuO4(6-) chromophore. We show that the differences in hue between these systems are controlled by a large red-shift (up to 7100 cm(-1)) produced by an electrostatic field created by a lattice over the CuO4(6-) chromophore from the energy of the 3z(2)-r(2) → x(2)-y(2) transition, a nonlocal phenomenon widely ignored in the realm of transition metal chemistry and strongly dependent upon the crystal structure. Along this line, we demonstrate that, although SiO4(4-) units are not involved in the chromophore itself, the introduction of sand to create CaCuSi4O10 plays a key role in obtaining the characteristic hue of the Egyptian Blue pigment. The results presented here demonstrate the opportunity for tuning the properties of a given chromophore by modifying the structure of the insulating lattice where it is located.

  4. Modeling turbulence structure. Chemical kinetics interaction in turbulent reactive flows

    Energy Technology Data Exchange (ETDEWEB)

    Magnussen, B.F. [The Norwegian Univ. of Science and Technology, Trondheim (Norway)

    1997-12-31

    The challenge of the mathematical modelling is to transfer basic physical knowledge into a mathematical formulation such that this knowledge can be utilized in computational simulation of practical problems. The combustion phenomena can be subdivided into a large set of interconnected phenomena like flow, turbulence, thermodynamics, chemical kinetics, radiation, extinction, ignition etc. Combustion in one application differs from combustion in another area by the relative importance of the various phenomena. The difference in fuel, geometry and operational conditions often causes the differences. The computer offers the opportunity to treat the individual phenomena and their interactions by models with wide operational domains. The relative magnitude of the various phenomena therefore becomes the consequence of operational conditions and geometry and need not to be specified on the basis of experience for the given problem. In mathematical modelling of turbulent combustion, one of the big challenges is how to treat the interaction between the chemical reactions and the fluid flow i.e. the turbulence. Different scientists adhere to different concepts like the laminar flamelet approach, the pdf approach of the Eddy Dissipation Concept. Each of these approaches offers different opportunities and problems. All these models are based on a sound physical basis, however none of these have general validity in taking into consideration all detail of the physical chemical interaction. The merits of the models can only be judged by their ability to reproduce physical reality and consequences of operational and geometric conditions in a combustion system. The presentation demonstrates and discusses the development of a coherent combustion technology for energy conversion and safety based on the Eddy Dissipation Concept by Magnussen. (author) 30 refs.

  5. Temperature effects on chemical structure and motion in coal

    Energy Technology Data Exchange (ETDEWEB)

    Maciel, G.E. [Colorado State Univ., Fort Collins, CO (United States). Dept. of Chemistry

    1996-06-01

    In this,report, we describe the first 1D and 2D {sup 1}H-{sup 1}H spin-exchange studies of coals based on {sup 1}H CRAMPS detection. We have designed and implemented a new 2D spin-exchange pulse sequence, which is able to probe complicated spin-exchange pathways among protons with different mobilities and chemical shifts. We demonstrate that 1D and 2D {sup 1}H-{sup 1}H spin-exchange experiments are very useful for studying extremely heterogeneous systems such as coals.

  6. Controlled modification of the structure of polymer surfaces by chemically grafting inorganic species

    Directory of Open Access Journals (Sweden)

    Rodrigo Lambert Oréfice

    1999-07-01

    Full Text Available Many chemical and physical methods, such as plasma, e-beam, sputtering, CVD and others, have been used to modify the structure of polymer surfaces by depositing thin inorganic films. Most of these techniques are based upon the use of high energy sources that ultimately can damage either chemically or physically polymer surfaces. Moreover, these methods are usually not versatile enough to allow the design of structurally and chemically tailored surfaces through the control of the distribution of chemical functionalities throughout the surface. In this work, inorganic species were introduced onto polymer substrates in a controlled manner by performing a sequence of chemical reactions at the surface. Sulfonation followed by silanization reactions were used to graft alkoxysilane species at the surface of poly(aryl sulfones. The heterogeneous chemical modification of poly(aryl sulfones was monitored by FTIR-ATR (Attenuated Total Reflection - FTIR. Model compounds were used to study the chemical reactions occurring during the grafting procedure. The results showed that the developed procedure can allow a controlled introduction of inorganic species onto polymer surfaces. Furthermore, in order to prove that this procedure enables the deposition of specific chemical functionalities onto polymer surfaces that can be used to create chemically and structurally tailored surfaces, silicate films were deposited on previously silanated PAS bioactive glass composites. In vitro tests showed that the surface modified composite can enhance the rates of hydroxy-carbonate-apatite precipitation.

  7. Chemical thermodynamics and elements of structure in oxide melts

    Science.gov (United States)

    Novikov, V. K.; Spiridonov, M. A.; Sangalova, I. S.

    2008-02-01

    The data analysis has shown that various structural elements of an oxide melt influence on a concrete property of a system differently. It is interesting to extract the elements with dominating influence on each property and elements with the negligible effect. We show that monomers SiO44- and ring structures Si4O128- do not influence neither on density, nor on the surface tension of the PbO-SiO2 system.

  8. Effect of Chemical Structure on Molecular Properties of Hyperbranched Polycarbosilanes

    Institute of Scientific and Technical Information of China (English)

    E.Tarabukina; A.Shpyrkov; A.Amirova; E.Tarasova; N.Shumilkina; A.Filippov; A.Muzafarov

    2007-01-01

    1 Results In spite of the increased interest to the synthesis of hyperbranched polymers,there is a lack of studies of conformational properties of their macromolecules.Structural features of hyperbranched polymers are responsible for new properties that distinguish them from linear compounds and open unique possibilities for their applications.The knowledge of the "structure-properties" relationships is of fundamental value,it also can be helpful when developing new technologies and new materials. The g...

  9. Corrosion inhibitors: Correlation between chemical structure and efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Lukovits, I.; Koszto, T. [Hungarian Academy of Sciences (Hungary). Inst. of Chemistry

    1999-11-01

    Corrosion inhibition efficiencies of heterocyclic aromatic or partially saturated aromatic compounds (pyrimidines, benzothiazole derivatives, amino-acids containing an aromatic part, pyridines and quinolines) were correlated with quan chemical indices of the respective molecules. Inhibition efficiencies measured in acidic solutions containing 0.001 and 0.01 mol/L of the inhibitor, respectively, were collected. The quantum chemical calculations were done by using the simple Hueckel method. Comparison of inhibition efficiencies and the differences between energies of the highest occupied and the lowest unoccupied molecular orbitals {Delta} indicated that if {Delta} is lower than 1.3 (in beta units) then the compound will not be active, whereas if {Delta} > 1.3 beta, the compound may be efficient in 0.001 mole/L concentration. The critical value of {Delta} may be lower in solution with 0.01 mole/L inhibitor concentration. Although {Delta} alone is not sufficient to account for the variation in the experimental inhibition efficiencies, the present result indicates that compounds which may be easily excited will be inefficient inhibitors because they maybe altered or decomposed after the excitation takes place.

  10. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    Science.gov (United States)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  11. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-11-15

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

  12. Energy flow in the cryptophyte PE545 antenna is directed by bilin pigment conformation.

    Science.gov (United States)

    Curutchet, Carles; Novoderezhkin, Vladimir I; Kongsted, Jacob; Muñoz-Losa, Aurora; van Grondelle, Rienk; Scholes, Gregory D; Mennucci, Benedetta

    2013-04-25

    Structure-based calculations are combined with quantitative modeling of spectra and energy transfer dynamics to detemine the energy transfer scheme of the PE545 principal light-harvesting antenna of the cryptomonad Rhodomonas CS24. We use a recently developed quantum-mechanics/molecular mechanics (QM/MM) method that allows us to account for pigment-protein interactions at atomic detail in site energies, transition dipole moments, and electronic couplings. In addition, conformational flexibility of the pigment-protein complex is accounted for through molecular dynamics (MD) simulations. We find that conformational disorder largely smoothes the large energetic differences predicted from the crystal structure between the pseudosymmetric pairs PEB50/61C-PEB50/61D and PEB82C-PEB82D. Moreover, we find that, in contrast to chlorophyll-based photosynthetic complexes, pigment composition and conformation play a major role in defining the energy ladder in the PE545 complex, rather than specific pigment-protein interactions. This is explained by the remarkable conformational flexibility of the eight bilin pigments in PE545, characterized by a quasi-linear arrangement of four pyrrole units. The MD-QM/MM site energies allow us to reproduce the main features of the spectra, and minor adjustments of the energies of the three red-most pigments DBV19A, DBV19B, and PEB82D allow us to model the spectra of PE545 with a similar quality compared to our original model (model E from Novoderezhkin et al. Biophys. J.2010, 99, 344), which was extracted from the spectral and kinetic fit. Moreover, the fit of the transient absorption kinetics is even better in the new structure-based model. The largest difference between our previous and present results is that the MD-QM/MM calculations predict a much smaller gap between the PEB50/61C and PEB50/61D sites, in better accord with chemical intuition. We conclude that the current adjusted MD-QM/MM energies are more reliable in order to explore the

  13. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  14. A proposed chemical structure for fructans from blue agave plant (Tequilana Weber var. azul)

    OpenAIRE

    Guillermo Toriz; Ezequiel Delgado; Virgilio Zúñiga

    2007-01-01

    A chemical structure for agave Tequilana fructans is proposed based upon the combined results of permethylation and reductive cleavage techniques coupled to gas-liquid chromatography (GLC), as well as size exclusión chromatography /lightscattering.

  15. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....... experimental data in the form of chemical shifts, as well as distance restraints obtained either experimentally or from sequence co-evolution. Of notable results, One of the determined structures, aKMT, was not solved experimentally at the time, but was found to match the recently published X-ray structure...

  16. Thermal supplies of Tarys Springs (South-East Tuva: profiles of micro-chemical structure

    Directory of Open Access Journals (Sweden)

    Choyganmaa K. Oydup

    2016-06-01

    Full Text Available Article presents the detailed geological specification of Tarys thermal springs area (Republic of Tuva, Russian Federation. Initial full micro-chemical structure of subsoil waters and Arzhaanets creek is presented.

  17. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    Science.gov (United States)

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  18. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    Science.gov (United States)

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  19. Structural Analysis Of Alfa Fibers After Chemical Treatment

    Directory of Open Access Journals (Sweden)

    Zakaria Mouallif

    2015-02-01

    Full Text Available Nowadays, natural fibers are used as reinforcement in composite materials. The Alfa fibers have undergone an alkaline treatment with sodium hydroxide NaOH at a concentration of 10%, during an immersion period of two days. After drying, the Fourier transform infrared spectroscopy by attenuated total reflection (FTIR-ATR and X-ray diffraction (XRD were used for the analysis of the chemical properties of these fibers which were extracted from the plant Alfa of the region Al Haouz (Morocco in order to study the modifications resulting from the alkaline treatment. The results proved the presence of the cellulose, with an increase in its proportion in those fibers which have undergone an alkaline treatment with NaOH, the presence of lignin and pectin, as well as their disappearance after the alkaline extraction.

  20. CHEMICALS

    CERN Document Server

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  1. Chemical Structures and Bioactivities of Sulfated Polysaccharides from Marine Algae

    Directory of Open Access Journals (Sweden)

    H. Stephen Ewart

    2011-02-01

    Full Text Available Sulfated polysaccharides and their lower molecular weight oligosaccharide derivatives from marine macroalgae have been shown to possess a variety of biological activities. The present paper will review the recent progress in research on the structural chemistry and the bioactivities of these marine algal biomaterials. In particular, it will provide an update on the structural chemistry of the major sulfated polysaccharides synthesized by seaweeds including the galactans (e.g., agarans and carrageenans, ulvans, and fucans. It will then review the recent findings on the anticoagulant/antithrombotic, antiviral, immuno-inflammatory, antilipidemic and antioxidant activities of sulfated polysaccharides and their potential for therapeutic application.

  2. Surface Nano-Structuring by Adsorption and Chemical Reactions

    OpenAIRE

    Ken-ichi Tanaka

    2010-01-01

    Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species are reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembl...

  3. Chemical thermodynamics and elements of structure in oxide melts

    Energy Technology Data Exchange (ETDEWEB)

    Novikov, V K; Spiridonov, M A; Sangalova, I S [Urals State Technical University-UPI, 620002, Mira 19, Ekaterinburg (Russian Federation)], E-mail: sma@mtf.ustu.ru

    2008-02-15

    The data analysis has shown that various structural elements of an oxide melt influence on a concrete property of a system differently. It is interesting to extract the elements with dominating influence on each property and elements with the negligible effect. We show that monomers SiO{sub 4}{sup 4-} and ring structures Si{sub 4}O{sub 12}{sup 8-} do not influence neither on density, nor on the surface tension of the PbO-SiO{sub 2} system.

  4. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  5. Impacts of chemical gradients on microbial community structure

    DEFF Research Database (Denmark)

    Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E

    2017-01-01

    Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox ...... Journal advance online publication, 17 January 2017; doi:10.1038/ismej.2016.175....

  6. Natural pigments and sacred art

    Science.gov (United States)

    Kelekian, Lena, ,, Lady

    2010-05-01

    Since the dawn of mankind, cavemen has expressed himself through art. The earliest known cave paintings date to some 32,000 years ago and used 4 colours derived from the earth. These pigments were iron oxides and known as ochres, blacks and whites. All pigments known by the Egyptians, the Greeks, the Romans and Renaissance man were natural and it was not until the 18th century that synthetic pigments were made and widely used. Until that time all art, be it sacred or secular used only natural pigments, of which the preparation of many have been lost or rarely used because of their tedious preparation. As a geologist, a mineralogist and an artist specializing in iconography, I have been able to rediscover 89 natural pigments extracted from minerals. I use these pigments to paint my icons in the traditional Byzantine manner and also to restore old icons, bringing back their glamour and conserving them for years to come. The use of the natural pigments in its proper way also helps to preserve the traditional skills of the iconographer. In the ancient past, pigments were extremely precious. Many took an exceedingly long journey to reach the artists, and came from remote countries. Research into these pigments is the work of history, geography and anthropology. It is an interesting journey in itself to discover that the blue aquamarines came from Afghanistan, the reds from Spain, the greens Africa, and so on. In this contribution I will be describing the origins, preparation and use of some natural pigments, together with their history and provenance. Additionally, I will show how the natural pigments are used in the creation of an icon. Being a geologist iconographer, for me, is a sacrement that transforms that which is earthly, material and natural into a thing of beauty that is sacred. As bread and wine in the Eucharist, water during baptism and oil in Holy Union transmit sanctification to the beholder, natural pigments do the same when one considers an icon. The

  7. Production of a Blue Pigment (Glaukothalin by Marine Rheinheimera spp.

    Directory of Open Access Journals (Sweden)

    Hans-Peter Grossart

    2009-01-01

    Full Text Available Two γ-Proteobacteria strains, that is, HP1 and HP9, which both produce a diffusible deep blue pigment, were isolated from the German Wadden Sea and from the Øresund, Denmark, respectively. Both strains affiliate with the genus Rheinheimera. Small amounts of the pigment could be extracted from HP1 grown in a 50 L fermenter and were purified chromatographically. Chemical analysis of the pigment including NMR and mass spectrometry led to a molecular formula of C34H56N4O4 (m.w. 584.85 which has not yet been reported in literature. The molecule is highly symmetrically and consists of two heterocyclic halves to which aliphatic side chains are attached. The pigment has been named glaukothalin due to its blue color and its marine origin (glaukos, gr.=blue, thalatta, gr.=sea. Production of glaukothalin on MB2216 agar plates by our Rheinheimera strains is affected in the presence of other bacterial strains either increasing or decreasing pigment production. The addition of a single amino acid, arginine (5 gl−1, greatly increases pigment production by our Rheinheimera strains. Even though the production of glaukothalin leads to inhibitory activity against three bacterial strains from marine particles, our Rheinheimera isolates are inhibited by various bacteria of different phylogenetic groups. The ecological role of glaukothalin production by Rheinheimera strains, however, remains largely unknown.

  8. Temperature effects on chemical structure and motion in coal. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Maciel, G.E.

    1996-09-30

    The objective of this project was to apply recently developed, state-of-the-art nuclear magnetic resonance (NMR) techniques to examine in situ changes in the chemical structure and molecular/macromolecular motion in coal as the temperature is increased above room temperature. Although alterations in the chemical structure of coal have been studied previously by {sup 13}C NMR, using quenched samples, the goal of this project was to examine these chemical structural changes, and changes in molecular/macromolecular mobility that may precede or accompany the chemical changes, at elevated temperatures, using modern {sup 13}C and {sup 1}H NMR techniques, especially {sup 1}H dipolar-dephasing techniques and related experiments pioneered in the laboratory for examining pyridine-saturated coals. This project consisted of the following four primary segments and related efforts on matters relevant to the first four tasks. (1) {sup 1}H NMR characterization of coal structure and mobility as a function of temperature variation over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (2) {sup 1}H NMR characterization of coal structure, mobility and conversion as a function of temperature variation over a temperature range (240--500 C) for which chemical transformations of coal are known to occur. (3) {sup 13}C NMR investigation of coal structure/mobility as a function of temperature over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (4) {sup 13}C NMR investigation of coal structure, dynamics and conversion as a function of temperature variation over a range (240--500 C) for which chemical transformations of coal are known to occur. (5) Related matters relevant to the first four tasks: (a) {sup 1}H CRAMPS NMR characterization of oil shales and their kerogen concentrates; and (b) improved quantitation in {sup 13}C MAS characterization of coals.

  9. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable

    Science.gov (United States)

    Werheit, Helmut

    2016-10-01

    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  10. Structural Change of Wood Molecules and Chemorheological Behaviors during Chemical Treatment

    Institute of Scientific and Technical Information of China (English)

    Xie Manhua; Zhao Guangjie

    2004-01-01

    It is very important to clarify the relationship of changes of molecular combinations in wood cell walls and the chemical rheological behavior during various chemical reagent treatments, for it would be helpful to develop new wood modification technologies and to enrich the theory of chemical rheology of wood. Based on previous investigations on the chemorheological properties of wood by chemical treatments and the applied methods in chemical rheology of wool fibers, this paper proposes the study of various additional reagents to wood saturated in water for long periods of time in order to investigate the chemical rheology of wood, which can provide information about the character of combinations between wood molecules and the structural changes of molecules and further put forward the idea of modifying wood in a decrystallized state.

  11. Multistable Phase Patterns of Spatially Structured Chemical Oscillators

    Science.gov (United States)

    Giver, Michael; Goldstein, Daniel; Chakraborty, Bulbul

    2014-03-01

    Recent experiments of two-dimensional microfluidic arrays of droplets containing Belousov-Zhabotinsky reactants show a rich variety of spatio-temporal patterns. Using optical techniques a variety of boundary conditions can be set within the system, including finite rings of droplets. These experiments have provided an interesting and easily reproducible system for probing the effects of nonlinearities and fluctuations in a spatially extended system. Motivated by this experimental set up, we study a simple model of chemical oscillators in the highly nonlinear excitable regime in order to gain insight into the mechanism giving rise to the observed multistable attractors. We map the attractor space of a simple two species activator-inhibitor model coupled via three different coupling mechanism: simple inhibitor diffusion, inhibitor diffusion through an inhomogenous medium where active droplets are separated by inactive holding cells, and coupling through diffusion of an inert signaling species, which arrises through a coarse graining of the inhomogenous medium. Once the attractor space of the mean-field level model has been mapped, we check the robustness of the attractors when subject to intrinsic noise.

  12. Brazilian kefir: structure, microbial communities and chemical composition

    Directory of Open Access Journals (Sweden)

    Karina Teixeira Magalhães

    2011-06-01

    Full Text Available Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5% were the major isolated group identified, followed by yeasts (30.6% and acetic acid bacteria (8.9%. Lactobacillus paracasei (89 isolates, Lactobacillus parabuchneri (41 isolates, Lactobacillus casei (32 isolates, Lactobacillus kefiri (31 isolates, Lactococcus lactis (24 isolates, Acetobacter lovaniensis (32 isolates, Kluyveromyces lactis (31 isolates, Kazachstania aerobia (23 isolates, Saccharomyces cerevisiae (41 isolates and Lachancea meyersii (15 isolates were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

  13. Brazilian kefir: structure, microbial communities and chemical composition

    Science.gov (United States)

    Magalhães, Karina Teixeira; de Melo Pereira, Gilberto Vinícius; Campos, Cássia Roberta; Dragone, Giuliano; Schwan, Rosane Freitas

    2011-01-01

    Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml. PMID:24031681

  14. Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Characterization of chemical structure.

    Science.gov (United States)

    Wang, Junlong; Yang, Wen; Wang, Jiancheng; Wang, Xia; Wu, Fang; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2015-11-20

    The biological activities of sulfated polysaccharides are related to the substitution positions of functional groups. In this study, regioselective sulfation of Artemisia sphaerocephala polysaccharides (SRSASP) was prepared by using triphenylchloromethane (TrCl) as protecting precursor. FT-IR spectra and X-ray photoelectron spectroscopy (XPS) showed that SO(3-) group (S(6+), high binding energy of 168.7eV) was widely present in sulfated polysaccharides. (13)C NMR spectroscopy showed that C-2 and C-3 substitution was occurred but not fully sulfation. Meanwhile, C-6 substituted signals near 65ppm were not observed. The degree of substitution varied from 0.44 to 0.63 in SRSASP which could be attributed to the low reactivity at secondary hydroxyl. Monosaccharide composition result showed a decrease in the ratio of mannose/glucose, indicating the change of chemical composition in sulfated polysaccharides. In size-exclusion chromatograph analysis, a decrease in molecular weight and broadening of molecular weight distribution of sulfated polysaccharides was also observed. It could be attributed to the hydrolysis of polysaccharide in the sulfated reaction.

  15. Inhibitors of Intracellular Signaling Pathways that Lead to Stimulated Epidermal Pigmentation: Perspective of Anti-Pigmenting Agents

    Directory of Open Access Journals (Sweden)

    Genji Imokawa

    2014-05-01

    Full Text Available Few anti-pigmenting agents have been designed and developed according to their known hyperpigmentation mechanisms and corresponding intracellular signaling cascades. Most anti-pigmenting agents developed so far are mechanistically involved in the interruption of constitutional melanogenic mechanisms by which skin color is maintained at a normal and unstimulated level. Thus, owing to the difficulty of confining topical application to a specific hyperpigmented skin area, potent anti-pigmenting agents capable of attenuating the natural unstimulated pigmentation process have the risk of leading to hypopigmentation. Since intracellular signaling pathways within melanocytes do not function substantially in maintaining normal skin color and are activated only by environmental stimuli such as UV radiation, specifically down-regulating the activation of melanogenesis to the constitutive level would be an appropriate strategy to develop new potent anti-pigmenting agents with a low risk of hypopigmentation. In this article, we review the hyperpigmentation mechanisms and intracellular signaling pathways that lead to the stimulation of melanogenesis. We also discuss a screening and evaluation system to select candidates for new anti-melanogenic substances by focusing on inhibitors of endothelin-1 or stem cell factor-triggered intracellular signaling cascades. From this viewpoint, we show that extracts of the herbs Withania somnifera and Melia toosendan and the natural chemicals Withaferin A and Astaxanthin are new candidates for potent anti-pigmenting substances that avoid the risk of hypopigmentation.

  16. Influence of temperature and dopant concentration on structural, morphological and optical properties of nanometric Ce1-xErxO2-δ (x = 0.05–0.20) as a pigment

    KAUST Repository

    Stojmenović, Marija

    2015-07-31

    Ceramic pigments based on cerium oxide were synthesized by self–propagating room temperature method and their color properties were assessed from the viewpoint of potential environmentally nontoxic pink pigments. Thermal stabilities of the pigments were examined at 600, 900 and 1200 ºC. According to X–ray powder diffraction and Raman spectroscopy results, all obtained pigments were single–phase solid solutions of cerium oxide, independent of the concentration of dopants. The X–ray analysis showed that the crystallites were of nanometric dimensions, as recorded and by transmission electron microscopy analysis. Color characteristics of solid solutions, which depended on concentracion erbium ions and calcination temperature, and their position in the chromaticity diagram were studied by ultraviolet–visible spectrophotometry, which confirmed potential application of environmentally friendly pigments of desired color. The color efficiency of pigments was also evaluated by colorimetric analysis.

  17. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures.

    Science.gov (United States)

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Castranova, Vincent; Porter, Dale W; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2015-12-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential.

  18. Zinc deficiency leads to lipofuscin accumulation in the retinal pigment epithelium of pigmented rats.

    Directory of Open Access Journals (Sweden)

    Sylvie Julien

    Full Text Available BACKGROUND: Age-related macular degeneration (AMD is associated with lipofuscin accumulation whereas the content of melanosomes decreases. Melanosomes are the main storage of zinc in the pigmented tissues. Since the elderly population, as the most affected group for AMD, is prone to zinc deficit, we investigated the chemical and ultrastructural effects of zinc deficiency in pigmented rat eyes after a six-month zinc penury diet. METHODOLOGY/PRINCIPAL FINDINGS: Adult Long Evans (LE rats were investigated. The control animals were fed with a normal alimentation whereas the zinc-deficiency rats (ZD-LE were fed with a zinc deficient diet for six months. Quantitative Energy Dispersive X-ray (EDX microanalysis yielded the zinc mole fractions of melanosomes in the retinal pigment epithelium (RPE. The lateral resolution of the analysis was 100 nm. The zinc mole fractions of melanosomes were significantly smaller in the RPE of ZD-LE rats as compared to the LE control rats. Light, fluorescence and electron microscopy, as well as immunohistochemistry were performed. The numbers of lipofuscin granules in the RPE and of infiltrated cells (Ø>3 µm found in the choroid were quantified. The number of lipofuscin granules significantly increased in ZD-LE as compared to control rats. Infiltrated cells bigger than 3 µm were only detected in the choroid of ZD-LE animals. Moreover, the thickness of the Bruch's membrane of ZD-LE rats varied between 0.4-3 µm and thin, rangy ED1 positive macrophages were found attached at these sites of Bruch's membrane or even inside it. CONCLUSIONS/SIGNIFICANCE: In pigmented rats, zinc deficiency yielded an accumulation of lipofuscin in the RPE and of large pigmented macrophages in the choroids as well as the appearance of thin, rangy macrophages at Bruch's membrane. Moreover, we showed that a zinc diet reduced the zinc mole fraction of melanosomes in the RPE and modulated the thickness of the Bruch's membrane.

  19. Elemental and mineralogical study of earth-based pigments using particle induced X-ray emission and X-ray diffraction

    Science.gov (United States)

    Nel, P.; Lynch, P. A.; Laird, J. S.; Casey, H. M.; Goodall, L. J.; Ryan, C. G.; Sloggett, R. J.

    2010-07-01

    Artwork and precious artefacts demand non-destructive analytical methodologies for art authentication, attribution and provenance assessment. However, structural and chemical characterisation represents a challenging problem with existing analytical techniques. A recent authentication case based on an Australian Aboriginal artwork, indicate there is substantial benefit in the ability of particle induced X-ray emission (PIXE), coupled with dynamic analysis (DA) to characterise pigments through trace element analysis. However, this information alone is insufficient for characterising the mineralogical residence of trace elements. For this reason a combined methodology based on PIXE and X-ray diffraction (XRD) has been performed to explore the benefits of a more comprehensive data set. Many Aboriginal paintings and artefacts are predominantly earth pigment based. This makes these cultural heritage materials an ideal case study for testing the above combined methodological approach on earth-based pigments. Samples of synthetic and naturally occurring earth-based pigments were obtained from a range of sources, which include Indigenous communities within Australia's Kimberley region. PIXE analyses using a 3 MeV focussed proton beam at the CSIRO nuclear microprobe, as well as laboratory-based XRD was carried out on the above samples. Elemental signature spectra as well as mineralogical data were used to assess issues regarding synthetic and naturally occurring earth pigments with the ultimate aim of establishing provenance.

  20. Fumed metallic oxides and conventional pigments for glossy inkjet paper

    Science.gov (United States)

    Lee, Hyunkook

    Product development activity in the area of inkjet printing papers has accelerated greatly to meet the rapidly growing market for inkjet papers. Advancements in inkjet printing technology have also placed new demands on the paper substrate due to faster printing rates, greater resolution through increased drop volumes, and colorants added to the ink. To meet these requirements, papermakers are turning to pigmented size press formulations or pigmented coating systems. For inkjet coating applications, both the internal porosity of the pigment particles as well as the packing porosity of the coating affect print quality and dry time. Pores between the pigment particles allow for rapid diffusion of ink fluids into the coating structure, while also providing capacity for ink fluid uptake. Past research has shown the presence of coating cracks to increase the microroughness of the papers, consequently reducing the gloss of the silica/polyvinyl alcohol based coating colors. Coating cracks were not observed, at the same level of magnification, in the scanning electron microscopy images of alumina/polyvinyl alcohol coated papers. Studies are therefore needed to understand the influence of coating cracking on the microroughening of silica/polyvinyl alcohol based coatings and consequences to coating and ink gloss. Since micro roughening is known to be linked to shrinkage of the coating layer, studies are needed to determine if composite pigments can be formulated, which would enable the coating solids of the formulations to be increased to minimize the shrinkage of coating layer during drying. Coating solids greater than 55% solids are needed to reduce the difference between application solids and the coating's immobilization solids point in order to reduce shrinkage. The aim of this research was to address the above mentioned needed studies. Studies were performed to understand the influence of particle packing on gloss and ink jet print quality. Composite pigment structures

  1. Convergent stereoselective synthesis of the visual pigment A2E.

    Science.gov (United States)

    Sicre, Cristina; Cid, M Magdalena

    2005-12-08

    [chemical reaction: see text]. A stereoselective total synthesis of the visual pigment A2E has been achieved with use of palladium-catalyzed cross-coupling reactions in all key steps: a regioselective Suzuki or Negishi coupling of 2,4-dibromopyridine, a Sonogashira reaction, and a double Stille cross-coupling to complete the bispolyenyl skeleton.

  2. Synthesis of Copper Pigments, Malachite and Verdigris: Making Tempera Paint

    Science.gov (United States)

    Solomon, Sally D.; Rutkowsky, Susan A.; Mahon, Megan L.; Halpern, Erica M.

    2011-01-01

    Malachite and verdigris, two copper-based pigments, are synthesized in this experiment intended for use in a general chemistry laboratory. The preparation of egg tempera paint from malachite is also described. All procedures can be done with a magnetic stir plate, standard glassware present in any first-year laboratory, and household chemicals.…

  3. Anthocyanins and Their Variation in Red Wines II. Anthocyanin Derived Pigments and Their Color Evolution

    Directory of Open Access Journals (Sweden)

    Chang-Qing Duan

    2012-02-01

    Full Text Available Originating in the grapes, anthocyanins and their derivatives are the crucial pigments responsible for the red wine color. During wine maturation and aging, the concentration of monomeric anthocyanins declines constantly, while numerous more complex and stable anthocyanin derived pigments are formed, mainly including pyranoanthocyanins, polymeric anthocyanins produced from condensation between anthocyanin and/or flavan-3-ols directly or mediated by aldehydes. Correspondingly, their structural modifications result in a characteristic variation of color, from purple-red color in young red wines to brick-red hue of the aged. Because of the extreme complexity of chemical compounds involved, many investigations have been made using model solutions of know composition rather than wine. Thus, there is a large amount of research still required to obtain an overall perspective of the anthocyanin composition and its change with time in red wines. Future findings may well greatly revise our current interpretation of the color in red wines. This paper summarizes the most recent advances in the studies of the anthocyanins derived pigments in red wines, as well as their color evolution.

  4. Anthocyanins and their variation in red wines. II. Anthocyanin derived pigments and their color evolution.

    Science.gov (United States)

    He, Fei; Liang, Na-Na; Mu, Lin; Pan, Qiu-Hong; Wang, Jun; Reeves, Malcolm J; Duan, Chang-Qing

    2012-02-07

    Originating in the grapes, anthocyanins and their derivatives are the crucial pigments responsible for the red wine color. During wine maturation and aging, the concentration of monomeric anthocyanins declines constantly, while numerous more complex and stable anthocyanin derived pigments are formed, mainly including pyranoanthocyanins, polymeric anthocyanins produced from condensation between anthocyanin and/or flavan-3-ols directly or mediated by aldehydes. Correspondingly, their structural modifications result in a characteristic variation of color, from purple-red color in young red wines to brick-red hue of the aged. Because of the extreme complexity of chemical compounds involved, many investigations have been made using model solutions of know composition rather than wine. Thus, there is a large amount of research still required to obtain an overall perspective of the anthocyanin composition and its change with time in red wines. Future findings may well greatly revise our current interpretation of the color in red wines. This paper summarizes the most recent advances in the studies of the anthocyanins derived pigments in red wines, as well as their color evolution.

  5. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta)

    Energy Technology Data Exchange (ETDEWEB)

    González, Aridane G., E-mail: aridaneglez@gmail.com [GET (Géosciences Environnement Toulouse) UMR 5563CNRS, 14 Avenue Edouard Belin, F-31400 Toulouse (France); Jimenez-Villacorta, Felix [Instituto de Ciencia de Materiales Madrid, CSIC, Cantoblanco, E-28049 Madrid (Spain); Beike, Anna K. [Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg (Germany); State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart (Germany); Reski, Ralf [Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg (Germany); BIOSS—Centre for Biological Signalling Studies, 79104 Freiburg (Germany); FRIAS—Freiburg Institute for Advanced Studies, 79104 Freiburg (Germany); Adamo, Paola [Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Naples (Italy); Pokrovsky, Oleg S. [GET (Géosciences Environnement Toulouse) UMR 5563CNRS, 14 Avenue Edouard Belin, F-31400 Toulouse (France); BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk (Russian Federation); Institute of Ecological Problems of the North, Russian Academy of Science, Arkhangelsk (Russian Federation)

    2016-05-05

    Highlights: • Cu{sup 2+} was adsorbed on four mosses used in moss-bag pollution monitoring technique. • Thermodynamic approach was used to model Cu speciation based on XAS results. • All studied mosses have ∼4.5 O/N atoms at ∼1.95 Å around Cu likely in a pseudo-square geometry. • Cu(II)-carboxylates and Cu(II)-phosphoryls are the main moss surface binding groups. • Moss growing in batch reactor yielded ∼20% of Cu(I) in the form of Cu–S(CN) complexes. - Abstract: The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05–0.06 mmolg{sub dry}{sup −1} and a maximal adsorption capacity of 0.93–1.25 mmolg{sub dry}{sup −1} for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu{sup 2+} yielded ∼20% of Cu(I) in the form of Cu–S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu{sup 2+}.

  6. Structural properties of produced CuO/NiO/glass thin layers Produced by chemical method

    Directory of Open Access Journals (Sweden)

    A. Ramezani

    2016-12-01

    Full Text Available Nickel Oxide and Copper oxide on Nickel Oxide thin layers were produced by chemical bath deposition method. There nano structures were investigated by SEM and EDAX analysis. By producing CuO/NiO/glass sandwich layers nano structure of NiO/glass layer changed and fraction of voids decreases. In sandwich layer physical property of outer layer was dominant

  7. Quantum chemical studies on structural, vibrational, nonlinear optical properties and chemical reactivity of indigo carmine dye

    Science.gov (United States)

    El-Mansy, M. A. M.

    2017-08-01

    Structural and vibrational spectroscopic studies were performed on indigo carmine (IC) isomers using FT-IR spectral analysis along with DFT/B3LYP method utilizing Gaussian 09 software. GaussView 5 program has been employed to perform a detailed interpretation of vibrational spectra. Simulation of infrared spectra has led to an excellent overall agreement with the observed spectral patterns. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NLO, first order hyperpolarizability and thermodynamic properties have been examined by (DFT/B3LYP) method with the SDD basis set level. Density of state spectra (DOS) were calculated using GaussSum 3 at the same level of theory. Molecular modeling approved that DOS Spectra are the most significant tools for differentiating between two IC isomers so far. Moreover, The IC isomers (cis-isomer) have shown an extended applicability for manufacturing both NLO and photovoltaic devices such as solar cells.

  8. Computer prediction of possible toxic action from chemical structure; the DEREK system.

    Science.gov (United States)

    Sanderson, D M; Earnshaw, C G

    1991-07-01

    1. The development of DEREK, a computer-based expert system (derived from the LHASA chemical synthesis design program) for the qualitative prediction of possible toxic action of compounds on the basis of their chemical structure is described. 2. The system is able to perceive chemical sub-structures within molecules and relate these to a rulebase linking the sub-structures with likely types of toxicity. 3. Structures can be drawn in directly at a computer graphics terminal or retrieved automatically from a suitable in-house database. 4. The system is intended to aid the selection of compounds based on toxicological considerations, or separately to indicate specific toxicological properties to be tested for early in the evaluation of a compound, so saving time, money and some laboratory animals and resources.

  9. Effect of mechanical activation on structure changes and reactivity in further chemical modification of lignin.

    Science.gov (United States)

    Zhao, Xiaohong; Zhang, Yanjuan; Hu, Huayu; Huang, Zuqiang; Yang, Mei; Chen, Dong; Huang, Kai; Huang, Aimin; Qin, Xingzhen; Feng, Zhenfei

    2016-10-01

    Lignin was treated by mechanical activation (MA) in a customized stirring ball mill, and the structure and reactivity in further esterification were studied. The chemical structure and morphology of MA-treated lignin and the esterified products were analyzed by chemical analysis combined with UV/vis spectrometer, FTIR,NMR, SEM and particle size analyzer. The results showed that MA contributed to the increase of aliphatic hydroxyl, phenolic hydroxyl, carbonyl and carboxyl groups but the decrease of methoxyl groups. Moreover, MA led to the decrease of particle size and the increase of specific surface area and roughness of surface in lignin. The reactivity of lignin was enhanced significantly for the increase of hydroxyl content and the improvement of mass transfer in chemical reaction caused by the changes of molecular structure and morphological structure. The process of MA is green and simple, and is an effective method for enhancing the reactivity of lignin. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. The relationship between chemical structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Hao [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States)]. E-mail: hao.jiang@wpafb.af.mil; Hong Lianggou [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States); Venkatasubramanian, N. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Grant, John T. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Eyink, Kurt [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Wiacek, Kevin [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Fries-Carr, Sandra [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Enlow, Jesse [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Bunning, Timothy J. [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States)

    2007-02-26

    Polymer dielectric films fabricated by plasma enhanced chemical vapor deposition (PECVD) have unique properties due to their dense crosslinked bulk structure. These spatially uniform films exhibit good adhesion to a variety of substrates, excellent chemical inertness, high thermal resistance, and are formed from an inexpensive, solvent-free, room temperature process. In this work, we studied the dielectric properties of plasma polymerized (PP) carbon-based polymer thin films prepared from two precursors, benzene and octafluorocyclobutane. Two different monomer feed locations, directly in the plasma zone or in the downstream region (DS) and two different pressures, 80 Pa (high pressure) or 6.7 Pa (low pressure), were used. The chemical structure of the PECVD films was examined by X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy. The dielectric constant ({epsilon} {sub r}) and dielectric loss (tan {delta}) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F {sub b}) was characterized by the current-voltage method. Spectroscopic ellipsometry was performed to determine the film thickness and refractive index. Good dielectric properties were exhibited, as PP-benzene films formed in the high pressure, DS region showed a F{sub b} of 610 V/{mu}m, an {epsilon} {sub r} of 3.07, and a tan {delta} of 7.0 x 10{sup -3} at 1 kHz. The PECVD processing pressure has a significant effect on final film structure and the film's physical density has a strong impact on dielectric breakdown strength. Also noted was that the residual oxygen content in the PP-benzene films significantly affected the frequency dependences of the dielectric constant and loss.

  11. 21 CFR 178.3725 - Pigment dispersants.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Pigment dispersants. 178.3725 Section 178.3725 Food... regulation, the substances listed in this section may be safely used as pigment dispersants in food-contact... not to exceed 0.45 percent by weight of the pigment. The pigmented articles may contact all...

  12. Extended Functional Groups (EFG: An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds

    Directory of Open Access Journals (Sweden)

    Elena S. Salmina

    2015-12-01

    Full Text Available The article describes a classification system termed “extended functional groups” (EFG, which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts of the On-line CHEmical database and Modeling (OCHEM environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models.

  13. Chemical structure, synthesis, and physical and chemical properties of porous polymers as materials applied in analytical chemistry and environmental protection

    Directory of Open Access Journals (Sweden)

    Goś Piotr

    2016-12-01

    Full Text Available This article is part of a series devoted to discussing strategies for the synthesis of ion-imprinted polymers and molecularly imprinted polymers, their chemical structure and great potential, which may be used in porous material design, analytical chemistry, environmental protection and other areas of science. The presented work constitutes a basis for a better understanding of what porous polymers are, how we can synthesise them and how to foresee their properties, which can be later used in studies of environmental pollution and analytical chemistry.

  14. Comparison of antioxidation systems of retinal pigment epithelium of pigmented and albino animals

    Energy Technology Data Exchange (ETDEWEB)

    Sakina, N.L.; Dontsov, A.E.; Ostrovskiy, M.A.

    1985-01-01

    The effectiveness of the lipid peroxidation inhibition process by tissue homogenates of retinal pigment epithelium of pigmented rabbits is higher than that of albino rabbits. The superoxide dismutase and glutathione perioxidase activity is nearly the same in both tissues of the pigment epithelium, the ..cap alpha..-tocopherol content is higher in retinal pigment epithelium tissue of albino animals, and the oxidizability of the lipid fraction of pigment epithelium tissue is higher in pigmented animals than in albinos. It is concluded that the higher resistance of the pigment epithelium of pigmented animals to the effects of prooxidant systems is due to the presence of melanoprotein granules in the pigment epithelium.

  15. Yellow and red ochre pigments from southern Portugal: Elemental composition and characterization by WDXRF and XRD

    Energy Technology Data Exchange (ETDEWEB)

    Gil, M. [Conservation and Restoration Department, Science and Technology Faculty, Univ. Nova of Lisbon, Monte da Caparica, 2829-516 Caparica (Portugal); Atomic Physics Center, Lisbon University, Av. Prof. Gama Pinto 2, 1649-003 Lisbon (Portugal)], E-mail: milenegil@gmail.com; Carvalho, M.L. [Atomic Physics Center, Lisbon University, Av. Prof. Gama Pinto 2, 1649-003 Lisbon (Portugal); Seruya, A. [Conservation and Restoration Department, Science and Technology Faculty, Univ. Nova of Lisbon, Monte da Caparica, 2829-516 Caparica (Portugal); Portuguese Institute of Conservation Restoration (IPCR), Rua das janelas Verdes 37, 1300-001 Lisbon (Portugal); Candeias, A.E. [Chemistry Department and Evora Chemistry Center, University of Evora, Rua Romao Ramalho, 59 Evora (Portugal); Mirao, J. [Giosciences Department and Evora Geophysics Center, University of Evora, Rua Romao Ramalho, 59 Evora (Portugal); Queralt, I. [Laboratory of X-ray Analytical Applications, Institute of Earth Sciences ' Jaume Almera' CSIC, Sole' Sabari' s s/n 08028 Barcelona (Spain)

    2007-09-21

    Three different yellow and red ochre pigments geological sources from Alentejo-Terras rossas, schist units and weathered iron ore deposits-were studied by elemental and phase analysis complemented with Munsell and CIELAB colour parameters. Central aims were to underline the mineralogical and chemical distinctiveness of natural pigment sources and establish a connection between local geology and use of specific colour pigments in traditional lime wash mural paintings. According to the chemical composition the Fe abundance is 6 times higher than average crust values. The Terras Rossas are characterized by higher Ca contents. In yellow and red schists, phyllosilicates are major minerals, so pigments from these units are enriched in K and Rb. Besides Fe, the pigments from weathered ores are enriched in metals like Pb, As, Cu, and Zn, which can be used as fingerprints.

  16. A pigmented calcifying odontogenic cyst.

    Science.gov (United States)

    Soames, J V

    1982-04-01

    A case of the pigmented variant of the calcifying odontogenic cyst occurring in a 15-year-old West Indian girl is reported. Melanin pigment was widely distributed and appeared in greatest amount in cells exhibiting the appearance of stellate reticulum. Ultrastructural examination demonstrated large numbers of melanosomes in these cells but relatively few in epithelial ghost cells. The latter contained thick bundles of tonofilaments. Melanocytes were identified and two forms were distinguished, depending on their content of premelanosomes and fully melanized melanosomes.

  17. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  18. Using a Microscale Approach to Rapidly Separate and Characterize Three Photosynthetic Pigment Species from Fern

    Science.gov (United States)

    Ayudhya, Theppawut Israsena Na; Posey, Frederick T.; Tyus, Jessica C.; Dingra, Nin N.

    2015-01-01

    A rapid separation of three photosynthetic pigments (chlorophyll "a" and "b" and xanthophyll) from fern ("Polystichum acrostichoides") is described using microscale solvent extraction and traditional thin layer chromatography that minimizes use of harmful chemicals and lengthy procedures. The experiment introduces…

  19. Cuticle structure in relation to chemical composition: re-assessing the prevailing model

    Directory of Open Access Journals (Sweden)

    Victoria eFernandez

    2016-03-01

    Full Text Available The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing towards the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth.

  20. Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model

    Science.gov (United States)

    Fernández, Victoria; Guzmán-Delgado, Paula; Graça, José; Santos, Sara; Gil, Luis

    2016-01-01

    The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing toward the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth. PMID:27066059

  1. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  2. Analysis of Indian pigment gallstones

    Energy Technology Data Exchange (ETDEWEB)

    Rautray, T.R. [Department of Physics, National Institute of Technology, Rourkela 769 008, Orissa (India)]. E-mail: tapash77@hotmail.com; Vijayan, V. [Institute of Physics, Bhubaneswar 751 005, Orissa (India); Panigrahi, S. [Department of Physics, National Institute of Technology, Rourkela 769 008, Orissa (India)

    2007-02-15

    Particle induced X-ray emission and particle induced {gamma}-ray emission spectroscopic techniques have been carried out to analyse the elemental concentrations of human pigment gallstone samples from eastern region (Orissa) and southern region (Chennai) of India. It was observed that 18 minor/trace elements namely Na, Mg, Al, P, S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Br and Pb were present in the pigment gallstone samples of both the regions. Our study reveals that average concentration of all elements except Ni in south Indian pigment gallstone samples is higher than that of corresponding values in east Indian pigment gallstone samples whereas elements like Al, P, S, Cl and V did not show much variation between these two regions. Fourier transform infra-red analysis was carried out to identify the functional groups and the classification of the pigment type gallstones of both the regions. The thermal behaviour of pigment gallstones was carried out by thermogravimetry-derivative thermogravimetry analysis.

  3. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    Science.gov (United States)

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-10-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  4. Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures.

    Science.gov (United States)

    Saeed, Faisal; Salim, Naomie; Abdo, Ammar

    2013-07-01

    Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures.

  5. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

    Science.gov (United States)

    Beck, Michael W; Derrick, Jeffrey S; Kerr, Richard A; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D; Kim, Kwang S; Lee, Joo-Yong; Ruotolo, Brandon T; Lim, Mi Hee

    2016-10-13

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  6. Construction of artificial pigment-protein antennae

    Energy Technology Data Exchange (ETDEWEB)

    Sibbald, JeNell [Iowa State Univ., Ames, IA (United States)

    1997-01-10

    Photosynthesis is a complex process which results in the conversion of solar radiation into chemical energy. This chemical energy is then used as the free energy source for all living organisms. In its basic form, photosynthesis can be described as the light-activated synthesis of carbohydrates from the simple molecules of water and carbon dioxide: 6H2O + 6 CO2 light C6H12O6 + 6 O2 This basic mechanism actually requires numerous reaction steps. The two primary steps being: the capture of light by pigment molecules in light-harvesting antenna complexes and the transfer of this captured energy to the so-called photochemical reaction center. While the preferred pathway for energy absorbed by the chromophores in the antenna complexes is transfer to the reaction center, energy can be lost to competing processes such as internal conversion or radiative decay. Therefore, the energy transfer must be rapid, typically on the order of picoseconds, to successfully compete. The focus of the present work is on the construction of light-harvesting antenna complexes incorporating modular pigment-proteins.

  7. A colorimetric sensor array of porous pigments.

    Science.gov (United States)

    Lim, Sung H; Kemling, Jonathan W; Feng, Liang; Suslick, Kenneth S

    2009-12-01

    The development of a low-cost, simple colorimetric sensor array capable of the detection and identification of toxic gases is reported. This technology uses a disposable printed array of porous pigments in which metalloporphyrins and chemically-responsive dyes are immobilized in a porous matrix of organically modified siloxanes (ormosils) and printed on a porous membrane. The printing of the ormosil into the membrane is highly uniform and does not lessen the porosity of the membrane, as shown by scanning electron microscopy. When exposed to an analyte, these pigments undergo reactions that result in well-defined color changes due to strong chemical interactions: ligation to metal ions, Lewis or Brønsted acid-base interactions, hydrogen bonding, etc. Striking visual identification of 3 toxic gases has been shown at the IDLH (immediately dangerous to life and health) concentration, at the PEL (permissible exposure level), and at a level well below the PEL. Identification and quantification of analytes were achieved using the color change profiles, which were readily distinguishable in a hierarchical clustering analysis (HCA) dendrogram, with no misclassifications in 50 trials.

  8. Improved Chemical Structure-Activity Modeling Through Data Augmentation.

    Science.gov (United States)

    Cortes-Ciriano, Isidro; Bender, Andreas

    2015-12-28

    Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spectroscopic data or the detection of conserved domains in protein sequences. In this contribution, we explore the effect of data augmentation in the predictive power of QSAR models, quantified by the RMSE values on the test set. We collected 8 diverse data sets from the literature and ChEMBL version 19 reporting compound activity as pIC50 values. The original training data were replicated (i.e., augmented) N times (N ∈ 0, 1, 2, 4, 6, 8, 10), and these replications were perturbed with Gaussian noise (μ = 0, σ = σnoise) on either (i) the pIC50 values, (ii) the compound descriptors, (iii) both the compound descriptors and the pIC50 values, or (iv) none of them. The effect of data augmentation was evaluated across three different algorithms (RF, GBM, and SVM radial) and two descriptor types (Morgan fingerprints and physicochemical-property-based descriptors). The influence of all factor levels was analyzed with a balanced fixed-effect full-factorial experiment. Overall, data augmentation constantly led to increased predictive power on the test set by 10-15%. Injecting noise on (i) compound descriptors or on (ii) both compound descriptors and pIC50 values led to the highest drop of RMSEtest values (from 0.67-0.72 to 0.60-0.63 pIC50 units). The maximum increase in predictive power provided by data augmentation is reached when the training data is replicated one time. Therefore, extending the original training data with one perturbed repetition thereof represents a reasonable trade-off between the increased performance of the models and the computational cost of data augmentation, namely increase of (i) model complexity due to the need for optimizing

  9. Chemical structures of constituents from the flowers of Osmanthus fragrans var. aurantiacus.

    Science.gov (United States)

    Liu, Jiang; Nakamura, Seikou; Xu, Bin; Matsumoto, Takahiro; Ohta, Tomoe; Fujimoto, Katsuyoshi; Ogawa, Keiko; Fukaya, Masashi; Miyake, Shiori; Yoshikawa, Masayuki; Matsuda, Hisashi

    2015-01-01

    Three new megastigmane glycosides named floraosmanosides I-III and a new γ-decalactone named floraosmanolactone I together with 16 known constituents were isolated from the flowers of Osmanthus fragrans var. aurantiacus cultivated in Guangxi Zhuang Autonomous Region, China. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. Among them, ligustroside and (+)-pinoresinol significantly inhibited nitric oxide production in lipopolysaccharide-activated RAW264.7 macrophages.

  10. Fluorescence, pigment and microscopic characterization of Bering Sea phytoplankton community structure and photosynthetic competency in the presence of a Cold Pool during summer

    Science.gov (United States)

    Goes, Joaquim I.; Gomes, Helga do Rosario; Haugen, Elin M.; McKee, Kali T.; D'Sa, Eurico J.; Chekalyuk, Alexander M.; Stoecker, Diane K.; Stabeno, Phyllis J.; Saitoh, Sei-Ichi; Sambrotto, Raymond N.

    2014-11-01

    Spectral fluorescence measurements of phytoplankton chlorophyll a (Chl a), phytoplankton phycobilipigments and variable fluorescence (Fv/Fm), are utilized with High Performance Liquid Chromatography (HPLC) estimates of phytoplankton pigments and microscopic cells counts to construct a comprehensive picture of summer-time phytoplankton communities and their photosynthetic competency in the eastern Bering Sea shelf. Although the Bering Sea was ice-free during our study, the exceptionally cold winter that preceded the summer of 2008 when our cruise took place, facilitated the formation of a "Cold Pool" (<2 °C) and its entrapment at depth in the northern middle shelf. The presence of a strong pycnocline over the entire middle and outer shelves restricted inorganic nutrient fluxes into the surface waters resulting in phytoplankton populations that were photo-physiologically stressed due to nutrient limitation. Elevated Chl a concentrations recorded in the Green Belt along the shelf edge of the Bering Sea, were due to Phaeocystis pouchetii and nano-sized cryptophytes. Although inorganic nutrients were not limiting in the Green Belt, Fv/Fm values were low in all probability due to iron limitation. Phytoplankton communities in the low biomass surface waters of the middle shelf were comprised of prasinophytes, haptophytes, cryptophytes and diatoms. In the northern part of the middle shelf, a sinking bloom made up of the centric diatoms Chaeotoceros socialis, Thalassiosira nordenskioeldii and Porosira glacialis was located above the Cold Pool. The high biomass associated with this senescent bloom and its accretion above the pycnocline, suggests that the Cold Pool acts as a barrier, preventing sinking phytoplankton from reaching the bottom where they can become available to benthic organisms. We further posit that if summer-time storms are not energetic enough and the Cold Pool is not eroded, its presence facilitates the transfer of the large spring phytoplankton bloom to

  11. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  12. Influence of the chemical structure of functional monomers on their adhesive performance.

    Science.gov (United States)

    Van Landuyt, K L; Yoshida, Y; Hirata, I; Snauwaert, J; De Munck, J; Okazaki, M; Suzuki, K; Lambrechts, P; Van Meerbeek, B

    2008-08-01

    Functional monomers in adhesive systems can improve bonding by enhancing wetting and demineralization, and by chemical bonding to calcium. This study tested the hypothesis that small changes in the chemical structure of functional monomers may improve their bonding effectiveness. Three experimental phosphonate monomers (HAEPA, EAEPA, and MAEPA), with slightly different chemical structures, and 10-MDP (control) were evaluated. Adhesive performance was determined in terms of microtensile bond strength of 4 cements that differed only for the functional monomer. Based on the Adhesion-Decalcification concept, the chemical bonding potential was assessed by atomic absorption spectrophotometry of the dissolution rate of the calcium salt of the functional monomers. High bond strength of the adhesive cement corresponded to low dissolution rate of the calcium salt of the respective functional monomer. The latter is according to the Adhesion-Decalcification concept, suggestive of a high chemical bonding capacity. We conclude that the adhesive performance of an adhesive material depends on the chemical structure of the functional monomer.

  13. Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster.

    Science.gov (United States)

    Dembeck, Lauren M; Huang, Wen; Magwire, Michael M; Lawrence, Faye; Lyman, Richard F; Mackay, Trudy F C

    2015-05-01

    Pigmentation varies within and between species and is often adaptive. The amount of pigmentation on the abdomen of Drosophila melanogaster is a relatively simple morphological trait, which serves as a model for mapping the genetic basis of variation in complex phenotypes. Here, we assessed natural variation in female abdominal pigmentation in 175 sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel, derived from the Raleigh, NC population. We quantified the proportion of melanization on the two most posterior abdominal segments, tergites 5 and 6 (T5, T6). We found significant genetic variation in the proportion of melanization and high broad-sense heritabilities for each tergite. Genome-wide association studies identified over 150 DNA variants associated with the proportion of melanization on T5 (84), T6 (34), and the difference between T5 and T6 (35). Several of the top variants associated with variation in pigmentation are in tan, ebony, and bric-a-brac1, genes known to affect D. melanogaster abdominal pigmentation. Mutational analyses and targeted RNAi-knockdown showed that 17 out of 28 (61%) novel candidate genes implicated by the genome-wide association study affected abdominal pigmentation. Several of these genes are involved in developmental and regulatory pathways, chitin production, cuticle structure, and vesicle formation and transport. These findings show that genetic variation may affect multiple steps in pathways involved in tergite development and melanization. Variation in these novel candidates may serve as targets for adaptive evolution and sexual selection in D. melanogaster.

  14. Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Lauren M Dembeck

    2015-05-01

    Full Text Available Pigmentation varies within and between species and is often adaptive. The amount of pigmentation on the abdomen of Drosophila melanogaster is a relatively simple morphological trait, which serves as a model for mapping the genetic basis of variation in complex phenotypes. Here, we assessed natural variation in female abdominal pigmentation in 175 sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel, derived from the Raleigh, NC population. We quantified the proportion of melanization on the two most posterior abdominal segments, tergites 5 and 6 (T5, T6. We found significant genetic variation in the proportion of melanization and high broad-sense heritabilities for each tergite. Genome-wide association studies identified over 150 DNA variants associated with the proportion of melanization on T5 (84, T6 (34, and the difference between T5 and T6 (35. Several of the top variants associated with variation in pigmentation are in tan, ebony, and bric-a-brac1, genes known to affect D. melanogaster abdominal pigmentation. Mutational analyses and targeted RNAi-knockdown showed that 17 out of 28 (61% novel candidate genes implicated by the genome-wide association study affected abdominal pigmentation. Several of these genes are involved in developmental and regulatory pathways, chitin production, cuticle structure, and vesicle formation and transport. These findings show that genetic variation may affect multiple steps in pathways involved in tergite development and melanization. Variation in these novel candidates may serve as targets for adaptive evolution and sexual selection in D. melanogaster.

  15. Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster

    Science.gov (United States)

    Dembeck, Lauren M.; Huang, Wen; Magwire, Michael M.; Lawrence, Faye; Lyman, Richard F.; Mackay, Trudy F. C.

    2015-01-01

    Pigmentation varies within and between species and is often adaptive. The amount of pigmentation on the abdomen of Drosophila melanogaster is a relatively simple morphological trait, which serves as a model for mapping the genetic basis of variation in complex phenotypes. Here, we assessed natural variation in female abdominal pigmentation in 175 sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel, derived from the Raleigh, NC population. We quantified the proportion of melanization on the two most posterior abdominal segments, tergites 5 and 6 (T5, T6). We found significant genetic variation in the proportion of melanization and high broad-sense heritabilities for each tergite. Genome-wide association studies identified over 150 DNA variants associated with the proportion of melanization on T5 (84), T6 (34), and the difference between T5 and T6 (35). Several of the top variants associated with variation in pigmentation are in tan, ebony, and bric-a-brac1, genes known to affect D. melanogaster abdominal pigmentation. Mutational analyses and targeted RNAi-knockdown showed that 17 out of 28 (61%) novel candidate genes implicated by the genome-wide association study affected abdominal pigmentation. Several of these genes are involved in developmental and regulatory pathways, chitin production, cuticle structure, and vesicle formation and transport. These findings show that genetic variation may affect multiple steps in pathways involved in tergite development and melanization. Variation in these novel candidates may serve as targets for adaptive evolution and sexual selection in D. melanogaster. PMID:25933381

  16. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

    NARCIS (Netherlands)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain

  17. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

    NARCIS (Netherlands)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

    2005-01-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architec

  18. Surface Nano Structures Manufacture Using Batch Chemical Processing Methods for Tooling Applications

    DEFF Research Database (Denmark)

    Tosello, Guido; Calaon, Matteo; Gavillet, J.

    2011-01-01

    The patterning of large surface areas with nano structures by using chemical batch processes to avoid using highenergy intensive nano machining processes was investigated. The capability of different surface treatment methods of creating micro and nano structured adaptable mould inserts...... for subsequent polymer replication by injection moulding was analyzed. New tooling solutions to produce nano structured mould surfaces were investigated. Experiments based on three different chemical-based-batch techniques to establish surface nano (i.e. sub-μm) structures on large areas were performed. Three...... approaches were selected: (1) using Ø500 nm nano beads deposition for direct patterning of a 4” silicon wafer; (2) using Ø500 nm nano beads deposition as mask for 4” silicon wafer etching and subsequent nickel electroplating; (3) using the anodizing process to produce Ø500 nm structures on a 30x80 mm2...

  19. Structural and chemical control in assembly of multicomponent metal-organic coordination networks on a surface.

    Science.gov (United States)

    Shi, Ziliang; Lin, Nian

    2010-08-11

    Surface-supported supramolecular self-assembly has been used to generate multicomponent two-dimensional metal-organic coordination networks on a Au(111) surface. The networks consist of linker ligands of 4',4''''-(1,4-phenylene)bis(2,2':6',2''-terpyridine) and nodal ligands of 5,10,15,20-tetra(4-pyridyl)porphyrin that are connected by pyridine-Fe-terpyridine motifs. Scanning tunneling microscopy revealed the coexistence of two polymorphic types of network structures (rhombus and Kagome). Through control of the dosage of the constituent ligands, homogeneous structural phases were obtained selectively. In particular, the rhombus structure could be converted into the more complex and more open Kagome structure by inclusion of guest molecules. Finally, coordination networks providing structural and chemical homogeneity were realized by judiciously choosing the dosages of the constituent ligands and the chemical substitution of the porphyrin ligands.

  20. Evaluación de la deformación de dos siliconas para prótesis faciales, influencia de la pigmentación y desinfección química Assessment of initial and the permanent deformation of two silicones (Silved Selant and Brascoved for facial prostheses under the pigmentation and chemical disinfection influence

    Directory of Open Access Journals (Sweden)

    Marcelo Goiato Coelho

    2010-06-01

    Full Text Available La propuesta de este estudio fue analizar el efecto de la pigmentación y de la desinfección química sobre la deformación inicial y permanente de dos siliconas (Silved Selant y Brascoved utilizadas en la confección de prótesis faciales. Las muestras para los analisis de deformación inicial y permanente (20 mm × 12,5 mm fueron confeccionadas de acuerdo con las instrucciones del fabricante. Para cada silicona (n= 40, diez muestras fueron pigmentadas con polvo de maquillaje, diez con óxido de hierro, diez con polvo de cerámica y diez sin pigmentación. Cinco muestras de cada grupo fueron sometidas a desinfección química, con clorhexidina al 2 % por aspersión. Todas las muestras fueron inmersas en suero fisiológico y almacenado en estufa a 35 º ± 1 ºC. Después de 90 días, las muestras fueron sometidas a los exámenes de deformación inicial y permanente. Para ambas propiedades, los datos fueron analizados por el test de Tukey (a= 0,05. Los resultados mostraron que todos los materiales presentaron deformación inicial y permanente independiente de la desinfección química y pigmentación. Los grupos pigmentados con óxido de hierro fueron los que presentaron menor deformación, inicial y permanente, cuando fueron sometidos a desinfección química, independientemente de la silicona usada.The purpose of present study was to analyze the effect of pigmentation and chemical disinfection on the initial and the permanent deformation of two silicones (Silved Selant and Brascoved for facial prosthesis. Initial and permanent deformation tests samples (20 mm × 12.5 mm were made following the manufacturer's instructions. For each silicone (n= 40, ten samples were used for pigmentation with make up power, ten with iron oxide, ten with ceramics power and tem were tested without pigmentation. Five samples of each group were submitted to chemical disinfection using a 2 % Chlorhexidine spray. All samples were immersed in physiological saline and

  1. Structured Process Energy-Exergy-Flow Diagram and Ideality Index for Analysis of Energy Transformation in Chemical Processes (Part 1)

    National Research Council Canada - National Science Library

    Hiroshi OAKI; Masaru ISHIDA; Tsuneo IKAWA

    1981-01-01

      A new diagram called structured process energy-exergy-flow diagram (SPEED) is proposed to systematically analyze the structure of energy flow in chemical processes and to design the process structures effectively...

  2. The effects of polymer pigmentation on fingermark development techniques.

    Science.gov (United States)

    Bacon, Simon R; Ojeda, Jesus J; Downham, Rory; Sears, Vaughn G; Jones, Benjamin J

    2013-11-01

    The effectiveness of latent fingerprint development techniques is heavily influenced by the physical and chemical properties of the deposition surface. The use of powder suspensions is increasing for development of prints on a range of surfaces. We demonstrate that carbon powder suspension development on polymers is detrimentally affected by the presence of common white pigment, titanium dioxide. Scanning electron microscopy demonstrates that patches of the compound are clearly associated with increased levels of powder adhesion. Substrates with nonlocalized titanium dioxide content also exhibit increased levels of carbon powder staining on a surface-wide basis. Secondary ion mass spectrometry and complementary techniques demonstrate the importance of levels of the pigment within the top 30 nm. The association is independent of fingermark deposition and may be related to surface energy variation. The detrimental effect of the pigment is not observed with small-particle reagent (MoS2 SPR) or cyanoacrylate (superglue) fuming techniques that exploit different development mechanisms.

  3. Generation of eye field/optic vesicle-like structures from human embryonic stem cells under two-dimensional and chemically defined conditions.

    Science.gov (United States)

    Parvini, Maryam; Parivar, Kazem; Safari, Fatemeh; Tondar, Mahdi

    2015-03-01

    Despite the enormous progress in studying retinal cell differentiation from human embryonic stem cells (hESCs), none of the reported protocols have produced a cost-effective eye field cells with the capability to further differentiate into retinal derivatives. In this study, by drawing chemicals on our four-step differentiation strategy, we demonstrated the ability of hESCs in assembling such qualifications to follow human retinogenesis in a serum- and feeder-free adherent condition. Two-dimensional (2D) populations of eye field cells arose within early forebrain progeny upon hESCs differentiation. Gene expression analysis showed that the treatment of hESCs with a combination of selected small molecules (SMs) gave rise to the higher expressions of eye field-specific genes, PAX6, RX, and SIX3. Thereafter, a subset of cells gained the transient features of advancing retinal differentiation, including optic vesicle (OV)-like structures, which expressed MITF and CHX10 in a manner imitated in vivo human retinal development. The competency of derived cells in differentiation to retinal derivatives was further investigated. The gene analysis of the cells showed more propensity for generating retinal pigment epithelial (RPE) than neural retina (NR). The generation of OV-like structures in 2D cultures can shed light on molecular events governing retinal specification. It can also facilitate the study of human retinal development.

  4. Application of chemical structure and bonding of actinide oxide materials for forensic science

    Energy Technology Data Exchange (ETDEWEB)

    Wilkerson, Marianne Perry [Los Alamos National Laboratory

    2010-01-01

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO{sub 2} (An: U, Pu) to form non-stoichiometric species described as AnO{sub 2+x}. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  5. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  6. Seeking carotenoid pigments in amber-preserved fossil feathers

    Science.gov (United States)

    Thomas, Daniel B.; Nascimbene, Paul C.; Dove, Carla J.; Grimaldi, David A.; James, Helen F.

    2014-06-01

    Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

  7. Chemical structure and physical properties of radiation-induced crosslinking of polytetrafluoroethylene

    Energy Technology Data Exchange (ETDEWEB)

    Oshima, Akihiro E-mail: aks@taka.jaeri.go.jp; Ikeda, Shigetoshi; Katoh, Etsuko; Tabata, Yoneho

    2001-07-01

    The chemical structure and physical properties of polytetrafluoroethylene (PTFE) that has been crosslinked by radiation have been studied by various methods. It has been found that a Y-type crosslinking structure and a Y-type structure incorporating a double bond (modified Y-type) is formed in PTFE by radiation-crosslinking in the molten state. In addition, various types of double bond structures, excluding the crosslinking site, have been identified. The crosslinked PTFE has a good light transparency due to the loss of crystallites, whilst it retains the excellent properties of electrical insulation and heat resistance. The coefficient of abrasion and the permanent creep are also greatly improved by crosslinking.

  8. Influence of Chemical Conditions on the Nanoporous Structure of Silicate Aerogels

    Directory of Open Access Journals (Sweden)

    Katalin Sinkó

    2010-01-01

    Full Text Available Silica or various silicate aerogels can be characterized by highly porous, open cell, low density structures. The synthesis parameters influence the three-dimensional porous structures by modifying the kinetics and mechanism of hydrolysis and condensation processes. Numerous investigations have shown that the structure of porous materials can be tailored by variations in synthesis conditions (e.g., the type of precursors, catalyst, and surfactants; the ratio of water/precursor; the concentrations; the medium pH; and the solvent. The objectives of this review are to summarize and elucidate the effects of chemical conditions on the nanoporous structure of sol-gel derived silicate aerogels.

  9. Bacterial Community Structure is Indicative of Chemical Inputs in the Upper Mississippi River

    Directory of Open Access Journals (Sweden)

    Christopher eStaley

    2014-10-01

    Full Text Available Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to > 40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of fourteen bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046 between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River.

  10. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  11. Evaluation of chemical and structural properties of germanium-carbon coatings deposited by plasma enhanced chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Jamali, Hossein, E-mail: h.jamali@mut-es.ac.ir; Mozafarinia, Reza; Eshaghi, Akbar

    2015-10-15

    Germanium-carbon coatings were deposited on silicon and glass substrates by plasma enhanced chemical vapor deposition (PECVD) using three different flow ratios of GeH{sub 4} and CH{sub 4} precursors. Elemental analysis, structural evaluation and microscopic investigation of coatings were performed using laser-induced breakdown spectroscopy (LIBS), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), Raman spectroscopy, field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM), respectively. Based on the results, the coatings exhibited a homogeneous and dense structure free of pores with a very good adhesion to substrate. The structural evaluation revealed that the germanium-carbon coatings were a kind of a Ge-rich composite material containing the amorphous and crystalline germanium and amorphous carbon with the mixture of Ge–Ge, Ge–C, C–C, Ge–H and C–H bonds. The result suggested that the amorphisation of the coatings could be increased with raising CH{sub 4}:GeH{sub 4} flow rate ratio and subsequently increasing C amount incorporated into the coating. - Highlights: • Germanium-carbon coatings were prepared by PECVD technique. • The germanium-carbon coatings were a kind of composite material. • The amorphisation of the coatings were increased with raising CH{sub 4}:GeH{sub 4} flow ratio.

  12. PPM-One: a static protein structure based chemical shift predictor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  13. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Brown, Nathan; Ertl, Peter; Jenkins, Jeremy L; Selzer, Paul; Hamon, Jacques

    2007-01-01

    Classification methods for data sets of molecules according to their chemical structure were evaluated for their biological relevance, including rule-based, scaffold-oriented classification methods and clustering based on molecular descriptors. Three data sets resulting from uniformly determined in vitro biological profiling experiments were classified according to their chemical structures, and the results were compared in a Pareto analysis with the number of classes and their average spread in the profile space as two concurrent objectives which were to be minimized. It has been found that no classification method is overall superior to all other studied methods, but there is a general trend that rule-based, scaffold-oriented methods are the better choice if classes with homogeneous biological activity are required, but a large number of clusters can be tolerated. On the other hand, clustering based on chemical fingerprints is superior if fewer and larger classes are required, and some loss of homogeneity in biological activity can be accepted.

  14. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure

    OpenAIRE

    Hollister, Kyle A.; Conner, Elizabeth S.; Zhang, Xinxing; Spell, Mark; Bernard, Gary M.; Patel, Pratik; de Carvalho, Ana Carolina G.V.; Butcher, Rebecca A.; Ragains, Justin R.

    2013-01-01

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This pane...

  15. EFFECT OF CHEMICAL STRUCTURE OF COMONOMERS ON THE PROPERTIES OF COPOLYESTERS

    Institute of Scientific and Technical Information of China (English)

    WU Rongrui; GAO Jing; LI Huiping

    1997-01-01

    The effect of different kinds of comonomers with or without flexible chain on properties of copolyesters, such as transition temperature, crystallization velocity, crystallinity and size of crystallites, is studied. The experimental results indicate the obvious difference in properties between comonomers with iso- and ortho-structure of phenyl ring and comonomers with flexible chain. The influence of chemical structure of comonomers on properties of copolyesters is discussed.

  16. Using Concept Mapping to Uncover Students' Knowledge Structures of Chemical Bonding Concepts

    Science.gov (United States)

    Burrows, Nikita L.; Mooring, Suazette Reid

    2015-01-01

    General chemistry is the first undergraduate course in which students further develop their understanding of fundamental chemical concepts. Many of these fundamental topics highlight the numerous conceptual interconnections present in chemistry. However, many students possess incoherent knowledge structures regarding these topics. Therefore,…

  17. Physico-Chemical and Structural Properties of DeNOx and SO2 Oxidation Catalysts

    DEFF Research Database (Denmark)

    Masters, Stephen Grenville; Oehlers, Cord; Nielsen, Kurt;

    1996-01-01

    Commercial catalysts for NOx removal and SO2 oxidation and their model systems have been investigated by spectroscopic, thermal, electrochemical and X-ray methods. Structural information on the vanadium complexes and compounds as well as physico-chemical properties for catalyst model systems have...... been obtained. The results are discussed in relation to proposed reaction mechanisms....

  18. Structural analysis of some marine kerogens through a combined chemical and thermal degradation approach

    NARCIS (Netherlands)

    Höld, I.M.

    2000-01-01

    Approximately 95% of the sedimentary organic matter in the geosphere exists in the form of kerogen, a macromolecular substance that is insoluble in water and normal organic solvents. There have been numerous attempts to elucidate the chemical structure of kerogens since kerogen is the main precursor

  19. Structures and Chemical Equilibria of Some N-Heterocycles Containing Amide Linkages

    Directory of Open Access Journals (Sweden)

    N. H. Abd El Moneim

    2003-05-01

    Full Text Available Structures and chemical equilibria of 5-carboxy-2-thiouracil (1, 5,6-diphenyl-3-hydroxy-1,2,4-triazine (2, 1-phenyl-3-methyl-5-pyrazolone (3 and 2-mercapto-4,6-dimethylpyrimidine hydrochloride (4 are reported. Their electronic transitions are assigned and pK values are evaluated and discussed.

  20. Correlation between chemical structure and rodent repellency of benzoic acid derivatives

    Science.gov (United States)

    Fearn, J.E.; DeWitt, J.B.

    1965-01-01

    Sixty-five benzoic acid derivatives were either prepared or obtained from commercial concerns, tested for rat repellency, and their indices of repellency computed. The data from these tests were considered analytically for any correlation between chemical structure and rat repellency. The results suggest a qualitative relationship which is useful in deciding probability of repellency in other compounds.

  1. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    Science.gov (United States)

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  2. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  3. Electronic Structure of Pi Systems: Part III--Applications in Spectroscopy and Chemical Reactivity.

    Science.gov (United States)

    Fox, Marye Anne; Matsen, F. A.

    1985-01-01

    Shows that electronic structure diagrams make more accurate predictions of spectral properties and chemical reactivity for simple pi systems than do either Huckel molecular orbital or valence bond theory alone. Topics addressed include absorption and photoelectron spectra, spin density distribution in radicals, and several problems regarding…

  4. Chemical structures and biological activities of bis- and tetrakis-acridine derivatives: A review

    Science.gov (United States)

    Nowak, Katarzyna

    2017-10-01

    A review of the literature on the biological activity of bis-acridines (diacridines) and tetrakis-acridines (tetra-acridines) is presented. Chemical structures of the most active derivatives are provided. In particular, the last decade's literature on the subject is discussed.

  5. Test results of chemical reactivity test (CRT) analysis of structural materials and explosives

    Energy Technology Data Exchange (ETDEWEB)

    Back, P.S.; Barnhart, B.V.; Walters, R.R.; Haws, L.D.; Collins, L.W.

    1980-03-21

    The chemical reactivity test, CRT, is a procedure used to screen the compatibility of component structure materials with explosives. This report contains the results of CRT materials evaluations conducted at Mound Facility. Data about materials combinations are catalogued both under the name of the explosive and the nonexplosive.

  6. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  7. Chemical signals turn on guest binding through structural reconfiguration of triangular helicates

    DEFF Research Database (Denmark)

    Sørensen, Anne; Castilla, Ana M.; Ronson, Tanya K.

    2013-01-01

    Be my guest: The function of a system based on self-assembled Zn(II) complexes can be controlled by external chemical stimuli. The complexes are based on a C3 -symmetric ligand that forms a unique triangular triple helicate structure 1. Upon subcomponent substitution, 1 is able to transform into ...

  8. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics.

    Science.gov (United States)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert

    2005-06-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architecture and natural product inspired compound library design. Domains and proteins identified as being structurally similar in their ligand-sensing cores are grouped in a protein structure similarity cluster (PSSC). Natural products can be considered as evolutionary pre-validated ligands for multiple proteins and therefore natural products that are known to interact with one of the PSSC member proteins are selected as guiding structures for compound library synthesis. Application of this novel strategy for compound library design provided enhanced hit rates in small compound libraries for structurally similar proteins.

  9. Bile pigments in pulmonary and vascular disease

    Directory of Open Access Journals (Sweden)

    Stefan W. Ryter

    2012-03-01

    Full Text Available The bile pigments, biliverdin and bilirubin, are endogenously-derived substances generated during enzymatic heme degradation. These compounds have been shown to act as chemical antioxidants in vitro. Bilirubin formed in tissues circulates in the serum, prior to undergoing hepatic conjugation and biliary excretion. The excess production of bilirubin has been associated with neurotoxicity, in particular to the newborn. Nevertheless, clinical evidence suggests that mild states of hyperbilirubinemia may be beneficial in protecting against cardiovascular disease in adults. Pharmacological application of either bilirubin and/or its biological precursor biliverdin, can provide therapeutic benefit in several animal models of cardiovascular and pulmonary disease. Furthermore, biliverdin and bilirubin can confer protection against ischemia/reperfusion injury and graft rejection secondary to organ transplantation in animal models. Several possible mechanisms for these effects have been proposed, including direct antioxidant and scavenging effects, and modulation of signaling pathways regulating inflammation, apoptosis, cell proliferation, and immune responses. The practicality and therapeutic-effectiveness of bile pigment application to humans remains unclear.

  10. Bile pigments in pulmonary and vascular disease.

    Science.gov (United States)

    Ryter, Stefan W

    2012-01-01

    The bile pigments, biliverdin, and bilirubin, are endogenously derived substances generated during enzymatic heme degradation. These compounds have been shown to act as chemical antioxidants in vitro. Bilirubin formed in tissues circulates in the serum, prior to undergoing hepatic conjugation and biliary excretion. The excess production of bilirubin has been associated with neurotoxicity, in particular to the newborn. Nevertheless, clinical evidence suggests that mild states of hyperbilirubinemia may be beneficial in protecting against cardiovascular disease in adults. Pharmacological application of either bilirubin and/or its biological precursor biliverdin, can provide therapeutic benefit in several animal models of cardiovascular and pulmonary disease. Furthermore, biliverdin and bilirubin can confer protection against ischemia/reperfusion injury and graft rejection secondary to organ transplantation in animal models. Several possible mechanisms for these effects have been proposed, including direct antioxidant and scavenging effects, and modulation of signaling pathways regulating inflammation, apoptosis, cell proliferation, and immune responses. The practicality and therapeutic-effectiveness of bile pigment application to humans remains unclear.

  11. Incorporation of codeine and metabolites into hair. Role of pigmentation.

    Science.gov (United States)

    Gygi, S P; Joseph, R E; Cone, E J; Wilkins, D G; Rollins, D E

    1996-04-01

    Xenobiotics circulating in the blood may become incorporated into growing hair. Melanin has affinity for many pharmacologically unrelated drugs and is responsible for the pigmentation in hair. To assess the role of pigmentation in the incorporation of drugs into hair, the distribution of codeine and its metabolites was studied in Sprague-Dawley (SD; white nonpigmented hair), Dark Agouti (DA; brown pigmented hair), and hooded Long-Evans (LE; both black pigmented and white nonpigmented hair) rats. Codeine was administered at a dose of 40 mg/kg/day i.p. for 5 days. Fourteen days after beginning the dosing protocol, hair was collected and analyzed for codeine, and its metabolite, morphine, by positive-ion chemical ionization GC/ion-trap MS. The plasma pharmacokinetics for codeine and morphine were also determined after a single 40 mg/kg injection (equivalent to first dose in 5-day dosing protocol) in all three strains of rats. Hair and plasma codeine and morphine concentrations were also determined after acid hydrolysis to evaluate the presence of glucuronide metabolites. Codeine concentrations in the hair of SD, DA, and pigmented LE hair were 0.98 +/- 0.10, 5.99 +/- 1.24, and 111.93 +/- 18.69 ng/mg hair, respectively; morphine concentrations were 0.34 +/- 0.04, 0.51 +/- 0.11, and 14.46 +/- 1.81 ng/mg hair, respectively; morphine glucuronide concentrations were 0.67 +/- 0.08, 1.04 +/- 0.37, and 13.80 +/- 3.60 ng/mg hair, respectively. Studies examining the in vitro binding of [3H] codeine and [3H]morphine to hair demonstrated both specific and nonspecific binding sites for codeine and morphine. Pigmented hair from LE rats possessed the greatest number of binding sites, white hair from SD rats contained the least, and brown hair from DA rats was intermediate. A time course study of codeine and its metabolites showed pigment-mediated differences in incorporation of codeine and metabolites within a few hours of drug administration. These data indicate that pigmented hair

  12. Photostability of Natural Orange-Red and Yellow Fungal Pigments in Liquid Food Model Systems

    DEFF Research Database (Denmark)

    Mapari, Sameer Shamsuddin; Meyer, Anne S.; Thrane, Ulf

    2009-01-01

    -red pigment extract was studied by high-performance liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS), and a light-induced formation of a structural analogue of sequoiamonascin C, a Monascus-like polyketide pigment discovered in the extract of Penicillium aculeatum IBT 14263 on yeast...

  13. Detailed evaluation of a newly attained fungal pigment from Monascus purpureus in meat burgers.

    Science.gov (United States)

    El-Kholie, Emad M; El Shaer, Magda K; Abdelreheem, Mohammed A T; Gharib, Mai A

    2012-11-01

    Beef burgers with red pigment extracted from Monascus purpureus, used as a natural colouring agent, were examined for chemical compositions, physical properties, microbiological aspects and organoleptic evaluation. Beef burgers with Monascus pigment showed higher nutritional values compared with control samples. Nutritional values were proportionally enhanced by increasing pigment concentration. Synthetic dye samples had the lowest values of nutrients. Cooking loss percentage and water holding capacity were lower in all treatments compared with control samples, and vice versa for plasticity. The initial total bacterial count, Staphylococcus aureus count and coliform count were determined. Extending storage period up to 90 days severely reduced all tested microorganisms. By increasing the M. pigment concentration, the colour was significantly increased. Insignificant differences in colours were noticed among various treatments. Flavour and body and texture scores were insignificantly different. Microbial inhibition percentage of beef burger samples was increased by increasing the Monascus pigment concentration up to 0.8 g/kg.

  14. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  15. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    Science.gov (United States)

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.

  16. Quantitative Survey and Structural Classification of Fracking Chemicals Reported in Unconventional Gas Exploitation

    Science.gov (United States)

    Elsner, Martin; Schreglmann, Kathrin

    2015-04-01

    additives reported for use in hydraulic fracturing. For the years 2005-2009 it is based on the Waxman report, and for the years 2011-2013 it relies on the database FracFocus, where it makes use of the data extracted and provided by the website "SkyTruth". For the first time, we list fracking chemicals according to their chemical structure and functional groups, because these properties are important as a starting point for (i) the design of analytical methods, (ii) to assess environmental fate and (iii) to understand why a given chemical is used at a certain stage of the fracturing process and what possible alternatives exist.

  17. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin.

    Science.gov (United States)

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-05-23

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their toxic side effects and increasing number of resistant pathogens set limits on their use. This review focuses on recent advances concerning quinolones and fluoroquinolones, we will be summarising chemical structure, mode of action, pharmacokinetic properties and toxicity. We will be describing fluoroquinolones introduced in clinical trials, namely avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and non-fluorinated nemonoxacin. These agents have been proved to have enhanced antibacterial effect even against ciprofloxacin resistant pathogens, and found to be well tolerated in both oral and parenteral administrations. These features are going to make them potential antimicrobial agents in the future.

  18. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    Science.gov (United States)

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.

  19. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  20. A Study on the Structural Analysis of Controllability in Chemical Processes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, B.W.; Kim, Y.S.; Yoon, E.S. [Division of Chemical Engineering, Seoul National University, Seoul (Korea)

    1999-04-01

    Chemical processes are highly nonlinear, multivariable systems and have complex structures. However, the controllability evaluation procedures are complicated, and the required information is very often unknown at the early design stage. Therefore, it is necessary to develop a procedure to evaluate and enhance controllability while designing processes and plants. To evaluate controllability in the design stage, it is most efficient to analyze process structure. Relative order can be used as a measure of 'physical closeness' between input and output variable. Structural controllability analysis using relative order is shown to be effective in a case study of heat exchanger network synthesis. 9 refs., 3 figs.

  1. The chemical and magnetic structures of holmium-yttrium and holmium-lutetium superlattices

    DEFF Research Database (Denmark)

    McMorrow, D.F.; Jehan, D.A.; Swaddling, P.P.;

    1993-01-01

    We present the results of a study of the chemical and magnetic structures of Ho/Y and Ho/Lu superlattices, all grown by molecular beam epitaxy. By combining the results of high-resolution X-ray diffraction with detailed modelling we show that the superlattices have high crystallographic integrity......: the average structural coherence length in the growth direction is approximately 2000 angstrom, while the interfaces between the two elements are well defined, extending over approximately four lattice planes. The magnetic structures were determined using neutron scattering techniques. In the case of the Ho...

  2. Nanostructured PLD-grown gadolinia doped ceria: Chemical and structural characterization by transmission electron microscopy techniques

    DEFF Research Database (Denmark)

    Rodrigo, Katarzyna Agnieszka; Wang, Hsiang-Jen; Heiroth, Sebastian

    2011-01-01

    The morphology as well as the spatially resolved elemental and chemical characterization of 10 mol% gadolinia doped ceria (CGO10) structures prepared by pulsed laser deposition (PLD) technique are investigated by scanning transmission electron microscopy accompanied with electron energy loss...... spectroscopy and energy dispersive X-ray spectroscopy. A dense, columnar and structurally inhomogeneous CGO10 film, i.e. exhibiting grain size refinement across the film thickness, is obtained in the deposition process. The cerium M4,5 edges, used to monitor the local electronic structure of the grains...

  3. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    Science.gov (United States)

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  4. Accuracy of pulse oximetry in pigmented patients

    African Journals Online (AJOL)

    Reflectance was measured at nine wavelengths. Results. The degree of pigmentation as measured by ... adversely affected by skin pigmentation, and it remains a ... the inner surface of the upper arm and the volar aspect of ..... Ph.D. mesis.

  5. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

    Science.gov (United States)

    Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

  6. Chemical structures of constituents from the whole plant of Bacopa monniera.

    Science.gov (United States)

    Ohta, Tomoe; Nakamura, Seikou; Nakashima, Souichi; Oda, Yoshimi; Matsumoto, Takahiro; Fukaya, Masashi; Yano, Mamiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2016-07-01

    Two new dammarane-type triterpene oligoglycosides, bacomosaponins A and B, and three new phenylethanoid glycosides, bacomosides A, B1, and B2, were isolated from the whole plant of Bacopa monniera Wettst. The chemical structures of the new constituents were characterized on the basis of chemical and physicochemical evidence. In the present study, bacomosaponins A and B with acyl groups were obtained from the whole plant of B. monniera. This is the first report of acylated dammarane-type triterpene oligoglycosides isolated from B. monniera. In addition, dammarane-type triterpene saponins significantly inhibited the aggregation of 42-mer amyloid β-protein.

  7. In situ chemical and structural investigations of the oxidation of Ge(001) substrates by atomic oxygen

    Science.gov (United States)

    Molle, Alessandro; Bhuiyan, Md. Nurul Kabir; Tallarida, Grazia; Fanciulli, Marco

    2006-08-01

    The exposure of Ge(001) substrates to atomic oxygen was studied in situ to establish the stability of the germanium oxide. After preparing chemically clean and atomically flat Ge(001) surfaces, the Ge samples were exposed to atomic oxygen in a wide temperature range from room temperature to 400°C. The chemical composition of the so-formed oxides was studied by means of x-ray photoelectron spectroscopy, while the structure was observed by reflection high energy electron diffraction. At low substrate temperatures the atomic oxygen is efficiently chemisorbed and suboxides coexist with the dioxide, which in turn is remarkably promoted in the high temperature range.

  8. Chemical structure of vanadium-based contact formation on n-AlN

    Energy Technology Data Exchange (ETDEWEB)

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  9. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    CERN Document Server

    van der Schaft, Arjan; Jayawardhana, Bayu

    2011-01-01

    Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set of equilibria and their stability properties. Furthermore, we develop a framework for interconnection of chemical reaction networks. Finally we discuss how the established framework leads to a new approach for model reduction.

  10. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

    Science.gov (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

    2015-11-01

    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  11. Clofazimine-induced Hair Pigmentation

    Science.gov (United States)

    Philip, Mariam; Samson, Joan Felicita; Simi, Puthenveedu Salahudeen

    2012-01-01

    A 45-year-old man was treated with WHO multibacillary multidrug therapy for borderline leprosy and high dose daily Clofazimine for lepra reaction. Along with the expected side effect of skin pigmentation, the patient also noticed darkening of previously grey hair. This colour persisted eight months after completing multibacillary multidrug therapy. PMID:23180930

  12. Clofazimine-induced Hair Pigmentation.

    Science.gov (United States)

    Philip, Mariam; Samson, Joan Felicita; Simi, Puthenveedu Salahudeen

    2012-07-01

    A 45-year-old man was treated with WHO multibacillary multidrug therapy for borderline leprosy and high dose daily Clofazimine for lepra reaction. Along with the expected side effect of skin pigmentation, the patient also noticed darkening of previously grey hair. This colour persisted eight months after completing multibacillary multidrug therapy.

  13. Primary pigmented nodular adrenocortical disease

    Directory of Open Access Journals (Sweden)

    Marie T Manipadam

    2011-01-01

    Full Text Available Primary pigmented nodular adrenocortical disease (PPNAD is a rare cause of ACTH-independent Cushing′s syndrome and has characteristic gross and microscopic pathologic findings. We report a case of PPNAD in a 15-year-old boy, which was not associated with Carney′s complex. Bilateral adrenalectomy is the treatment of choice.

  14. Isolation and structure of a novel charged member of the red-pigment-concentrating hormone-adipokinetic hormone family of peptides isolated from the corpora cardiaca of the blowfly Phormia terraenovae (Diptera).

    Science.gov (United States)

    Gäde, G; Wilps, H; Kellner, R

    1990-01-01

    A hypertrehalosaemic neuropeptide from the corpora cardiaca of the blowfly Phormia terraenovae has been isolated by reversed-phase h.p.l.c., and its primary structure was determined by pulsed-liquid phase sequencing employing Edman chemistry after enzymically deblocking the N-terminal pyroglutamate residue. The C-terminus was also blocked, as indicated by the lack of digestion when the peptide was incubated with carboxypeptidase A. The octapeptide has the sequence pGlu-Leu-Thr-Phe-Ser-Pro-Asp-Trp-NH2 and is clearly defined as a novel member of the RPCH/AKH (red-pigment-concentrating hormone/adipokinetic hormone) family of peptides. It is the first charged member of this family to be found. The synthetic peptide causes an increase in the haemolymph carbohydrate concentration in a dose-dependent fashion in blowflies and therefore is named 'Phormia terraenovae hypertrehalosaemic hormone' (Pht-HrTH). In addition, receptors in the fat-body of the American cockroach (Periplaneta americana) recognize the peptide, resulting in carbohydrate elevation in the blood. However, fat-body receptors of the migratory locust (Locusta migratoria) do not recognize this charged molecule, and thus no lipid mobilization is observed in this species. PMID:2386478

  15. Structure of Pigment Yellow 181 dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate from XRPD plus DFT-D

    DEFF Research Database (Denmark)

    van de Streek, Jacco

    2015-01-01

    -pyrrolidone (1:1:1) solvate. The crystal structure, which in principle has 28 possible degrees of freedom, was determined in three stages by a combination of simulated annealing, partial Rietveld refinement with dummy atoms replacing the solvent molecules and further simulated annealing. The phase not being...

  16. Evaluation of shape and size effects on optical properties of ZnO pigment

    Energy Technology Data Exchange (ETDEWEB)

    Kiomarsipour, Narges, E-mail: na.kiomarsipour@yahoo.com [Department of Materials Engineering, Malek Ashtar University of Technology, Shahin Shahr P.O. Box 83145/115, Isfahan (Iran, Islamic Republic of); Shoja Razavi, Reza [Department of Materials Engineering, Malek Ashtar University of Technology, Shahin Shahr P.O. Box 83145/115, Isfahan (Iran, Islamic Republic of); Ghani, Kamal [Department of Chemistry, Malek Ashtar University of Technology, Shahin Shahr P.O. Box 83145/115, Isfahan (Iran, Islamic Republic of); Kioumarsipour, Marjan [Department of Physics, University of Kashan, Kashan (Iran, Islamic Republic of)

    2013-04-01

    The pigment with optimized morphology would attain maximum diffuse solar reflectance at a lower film thickness and reduce the pigment volume concentration required. This factor would contribute to a reduction in overall weight and possibly extend the durability of the system to longer time scales, specially in space assets. In the present work, five different morphologies of ZnO pigment were synthesized by hydrothermal method. The ZnO pigments were characterized by X-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM) and N{sub 2} adsorption (BET). The optical property of the ZnO pigments was investigated by UV/VIS/NIR spectrophotometer. The results indicated that the optical properties of ZnO powders were strongly affected by the particle size and morphology. The nanorods and microrods ZnO structures showed the minimum spectral reflectance in visible and near infrared regions, whereas the novel nanoparticle-decorated ZnO pigment revealed the maximum spectral reflectance in the same regions. The reflectance spectra of scale-like and submicrorods ZnO were in the middle of the others. The higher surface roughness led to higher light scattering in nanoparticle-decorated ZnO pigment and multiple-scattering in them. These results proved that a significant improvement in the scattering efficiency of ZnO pigment can be realized by utilizing an optimized nanoparticle-decorated pigment.

  17. Pigments from UV-resistant Antarctic bacteria as photosensitizers in Dye Sensitized Solar Cells.

    Science.gov (United States)

    Órdenes-Aenishanslins, N; Anziani-Ostuni, G; Vargas-Reyes, M; Alarcón, J; Tello, A; Pérez-Donoso, J M

    2016-09-01

    Here we report the use of pigments produced by UV-resistant Antarctic bacteria as photosensitizers in Dye Sensitized Solar Cells (DSSCs). Pigments were obtained from red and yellow colored psychrotolerant bacteria isolated from soils of King George Island, Antarctica. Based on metabolic characteristics and 16s DNA sequence, pigmented bacteria were identified as Hymenobacter sp. (red) and Chryseobacterium sp. (yellow). Pigments produced by these microorganisms were extracted and classified as carotenoids based on their spectroscopic and structural characteristics, determined by UV-Vis spectrophotometry and infrared spectroscopy (FTIR), respectively. With the purpose of develop green solar cells based on bacterial pigments, the photostability and capacity of these molecules as light harvesters in DSSCs were determined. Absorbance decay assays determined that bacterial carotenoids present high photostability. In addition, solar cells based on these photosensitizers exhibit an open circuit voltage (VOC) of 435.0 [mV] and a short circuit current density (ISC) of 0.2 [mA·cm(-2)] for the red pigment, and a VOC of 548.8 [mV] and a ISC of 0.13 [mA·cm(-2)] for the yellow pigment. This work constitutes the first approximation of the use of pigments produced by non-photosynthetic bacteria as photosensitizers in DSSCs. Determined photochemical characteristics of bacterial pigments, summed to their easy obtention and low costs, validates its application as photosensitizers in next-generation biological solar cells.

  18. Accumulation of yellow Monascus pigments by extractive fermentation in nonionic surfactant micelle aqueous solution.

    Science.gov (United States)

    Xiong, Xu; Zhang, Xuehong; Wu, Zhenqiang; Wang, Zhilong

    2015-02-01

    Monascus species can produce various secondary metabolites of polyketide structure. In the current study, it is found that an interesting phenomenon, i.e., submerged culture of Monascus species in an aqueous solution majorly accumulated intracellular orange Monascus pigments exhibiting one peak at 470 nm with absorbance of 32 OD while extractive fermentation in a nonionic surfactant micelle aqueous solution produced extracellular and intracellular yellow Monascus pigments exhibiting one peak at 410 nm with absorbance 30 OD and 12 OD, respectively. The spectrum profiles of both intracellular and extracellular Monascus pigments were affected by surfactant loading, extractive fermentation time, and surfactant adding time. Meanwhile, the instability of orange Monascus pigments in the extracellular nonionic surfactant micelle aqueous solution was also confirmed experimentally. The mechanism behind this phenomenon is attributed to the export of intracellular yellow Monascus pigments into its broth by extractive fermentation. The transferring of intracellular yellow Monascus pigments into its broth blocks yellow Monascus pigments from further enzymatic conversion or eliminates the feedback inhibition of yellow Monascus pigments based on the biosynthetic pathway of Monascus pigments.

  19. Pigmentation associated histopathological variations in sympathetic ophthalmia.

    Science.gov (United States)

    Marak, G E; Ikui, H

    1980-01-01

    The severity of inflammation in sympathetic ophthalmia is related to the degree of pigmentation, and the granulomatous response seems to be related to pigmentation. Eosinophilia is also associated with pigmentation, but this association appears to be fortuitous and is a result of the association of eosinophilia with severity of the inflammation. PMID:7387955

  20. 21 CFR 73.352 - Paracoccus pigment.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Paracoccus pigment. 73.352 Section 73.352 Food and... ADDITIVES EXEMPT FROM CERTIFICATION Foods § 73.352 Paracoccus pigment. (a) Identity. (1) The color additive... mixtures for coloring foods. (b) Specifications. Paracoccus pigment shall conform to the...

  1. A case of pigmented Bowen's disease*

    Science.gov (United States)

    Vivan, Márcia Maria; Hirata, Sérgio Henrique; do Nascimento, Liliane Santos; Enokihara, Milvia Maria Simões e Silva

    2017-01-01

    Pigmented Bowen's disease is a rare subtype of Bowen's disease. Clinically it presents as a slow-growing, well-defined, hyperpigmented plaque, and should be included as a differential diagnosis of other pigmented lesions. The authors describe a challenging case of pigmented Bowen's disease with non-diagnostic dermscopy findings. PMID:28225972

  2. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    Science.gov (United States)

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  3. Solubilization capacity of nonionic surfactant micelles exhibiting strong influence on export of intracellular pigments in Monascus fermentation

    Science.gov (United States)

    Kang, Biyu; Zhang, Xuehong; Wu, Zhenqiang; Qi, Hanshi; Wang, Zhilong

    2013-01-01

    Summary In this study, perstractive fermentation of intracellular Monascus pigments in nonionic surfactant micelle aqueous solution had been studied. The permeability of cell membrane modified by nonionic surfactant might have influence on the rate of export of intracellular pigments into its extracellular broth while nearly no effect on the final extracellular pigment concentration. However, the solubilization of pigments in nonionic surfactant micelles strongly affected the final extracellular pigment concentration. The solubilization capacity of micelles depended on the kind of nonionic surfactant, the super-molecule assembly structure of nonionic surfactant in an aqueous solution, and the nonionic surfactant concentration. Elimination of pigment degradation by export of intracellular Monascus pigments and solubilizing them into nonionic surfactant micelles was also confirmed experimentally. Thus, nonionic surfactant micelle aqueous solution is potential for replacement of organic solvent for perstractive fermentation of intracellular product. PMID:23425092

  4. Solubilization capacity of nonionic surfactant micelles exhibiting strong influence on export of intracellular pigments in Monascus fermentation.

    Science.gov (United States)

    Kang, Biyu; Zhang, Xuehong; Wu, Zhenqiang; Qi, Hanshi; Wang, Zhilong

    2013-09-01

    In this study, perstractive fermentation of intracellular Monascus pigments in nonionic surfactant micelle aqueous solution had been studied. The permeability of cell membrane modified by nonionic surfactant might have influence on the rate of export of intracellular pigments into its extracellular broth while nearly no effect on the final extracellular pigment concentration. However, the solubilization of pigments in nonionic surfactant micelles strongly affected the final extracellular pigment concentration. The solubilization capacity of micelles depended on the kind of nonionic surfactant, the super-molecule assembly structure of nonionic surfactant in an aqueous solution, and the nonionic surfactant concentration. Elimination of pigment degradation by export of intracellular Monascus pigments and solubilizing them into nonionic surfactant micelles was also confirmed experimentally. Thus, nonionic surfactant micelle aqueous solution is potential for replacement of organic solvent for perstractive fermentation of intracellular product.

  5. Effect of chemical substituents on the structure of glassy diphenyl polycarbonates.

    Science.gov (United States)

    Sulatha, M S; Natarajan, Upendra

    2011-02-24

    Polycarbonates offer a wide variety of physical property behavior that is difficult to predict due to complexities at the molecular scale. Here, the physical structure of amorphous glassy polycarbonates having aliphatic and cycloaliphatic chemical groups is explored through atomistic simulations. The influence of chemical structure on solubility parameter, torsion distributions, radial distribution function, scattering structure factor, orientation distributions of phenylene rings and carbonate groups, and free volume distributions, leading to interchain packing effects, are shown. The effect of the cyclohexyl ring at the isopropylidene carbon as compared to the effect of the methyl groups positioned on the phenylene rings results in a larger reduction in the solubility parameter (δ). The interchain distance estimated for polycarbonates in this work is in the range of 5-5.8 Å. The o-methyl groups on the phenylene rings, as compared to a cyclohexyl ring, lead to higher interchain distances. The highest interchain distance is observed with a trimethylcyclohexylidene group at the isopropylidene carbon. Atomistic simulations reveal two different types of packing arrangement of nearest-neighbor chains in the glassy state, one type of which agrees with the NMR experimental data. The fundamental insights provided here can be utilized for design of chemical structures for tailored macroscopic properties.

  6. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

    Directory of Open Access Journals (Sweden)

    Ville Y. P. Väre

    2017-03-01

    Full Text Available RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  7. Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

    Science.gov (United States)

    Berns, Veronica M; Fredrickson, Daniel C

    2014-10-06

    Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

  8. Protein structure similarity clustering and natural product structure as guiding principles for chemical genomics.

    Science.gov (United States)

    Koch, M A; Waldmann, H

    2006-01-01

    The majority of all proteins are modularly built from a limited set of approximately 1,000 structural domains. The knowledge of a common protein fold topology in the ligand-sensing cores of protein domains can be exploited for the design of small-molecule libraries in the development of inhibitors and ligands. Thus, a novel strategy of clustering protein domain cores based exclusively on structure similarity considerations (protein structure similarity clustering, PSSC) has been successfully applied to the development of small-molecule inhibitors of acetylcholinesterase and the 11beta-hydroxysteroid dehydrogenases based on the structure of a naturally occurring Cdc25 inhibitor. The efficiency of making use of the scaffolds of natural products as biologically prevalidated starting points for the design of compound libraries is further highlighted by the development of benzopyran-based FXR ligands.

  9. Development of new materials and structures based on managed physical-chemical factors of local interaction

    Science.gov (United States)

    Urakov, A. L.

    2016-04-01

    The paper states that assigning certain physical and chemical characteristics to pills and medical drugs solutions can substitute for the development of new drugs (which is essentially equivalent to the creation of new medicines). It is established that the purposeful change of physical and chemical characteristics of the standard ("old") materials (in other words, the known substances) is fundamental for the production of solid and liquid medicines, which allows us to get "new" structures and materials. The paper shows that assigning new physical and chemical properties to "old" materials and their further usage for the production of tablets and solutions from the "old" and well-known medicines can turn even very "old" medicine into very "novel" (moreover, even very fashionable) one with unprecedented (fantastic) pharmacological activity and new mechanisms of action.

  10. Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

    Science.gov (United States)

    Batke, Monika; Gütlein, Martin; Partosch, Falko; Gundert-Remy, Ursula; Helma, Christoph; Kramer, Stefan; Maunz, Andreas; Seeland, Madeleine; Bitsch, Annette

    2016-01-01

    Interest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g., the European Union's Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database, and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural, and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT) approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (cluster and to use this information for a

  11. Relationships between chemical structure, mechanical properties and materials processing in nanopatterned organosilicate fins

    Directory of Open Access Journals (Sweden)

    Gheorghe Stan

    2017-04-01

    Full Text Available The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM to investigate the fabrication of 20–500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10–20 nm. While the observed structure–property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential.

  12. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure.

    Science.gov (United States)

    Hollister, Kyle A; Conner, Elizabeth S; Zhang, Xinxing; Spell, Mark; Bernard, Gary M; Patel, Pratik; de Carvalho, Ana Carolina G V; Butcher, Rebecca A; Ragains, Justin R

    2013-09-15

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This panel includes a number of natural ascarosides that were detected in crude pheromone extract, but as yet have no assigned function, as well as many unnatural ascaroside derivatives. Most of these ascarosides, some of which have significant structural similarity to the natural dauer pheromone components, have very little dauer-inducing activity. Our results provide a primer to ascaroside structure-activity relationships and suggest that slight modifications to ascaroside structure dramatically influence binding to the relevant G protein-coupled receptors that control dauer formation.

  13. Study on the Pigments of the Colored Cotton

    Institute of Scientific and Technical Information of China (English)

    GU Zhao-wen; SHI Song-cun

    2004-01-01

    The ecological characteristics and fiber structure of the colored cotton were introduced briefly. The color changing mechanisms of the pigments extracted from colored cottons and some plants were discussed with the results of different experiments, which could offer an academic reference for the color fixations of the colored cotton textile produces and promote the development of the natural colored cotton industry.

  14. Analysis of pigments from Roman wall paintings found in Vicenza.

    Science.gov (United States)

    Mazzocchin, G A; Agnoli, F; Mazzocchin, S; Colpo, I

    2003-11-12

    The analysis of about 60 samples of wall paintings was carried out using different chemicophysical techniques: optical microscopy, scanning electron microscopy (SEM) equipped with an EDS microanalysis detector, X-ray powder diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The identified pigments were cinnabar, hematite, red ochre, celadonite, cuprorivaite (Egyptian blue), yellow ochre, goethite and carbon. Only in one case some lead white was found instead. In general, the mortar preparation did not correspond to the complex structure suggested by Vitruvius (De Architectura), but it generally showed a porous layer, with crushed grains under the pigment layer. In certain cases two superposed pigment layers were found: yellow superimposed on both red and pink, black on pink, green on black.

  15. Chemical-mechanical stability of the hierarchical structure of shell nacre

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The hierarchical structure and mechanical property of shell nacre are experimentally investigated from the new aspects of chemical stability and chemistry-mechanics coupling. Through chemical deproteinization or demineralization methods together with characterization techniques at micro/nano scales,it is found that the nacre of abalone,haliotis discus hannai,contains a hierarchical structure stacked with irregular aragonite platelets and interplatelet organic matrix thin layers. Yet the aragonite platelet itself is a nanocomposite consisting of nanoparticles and intraplatelet organic matrix framework. The mean diameter of the nanoparticles and the distribution of framework are quite different for different platelets. Though the interplatelet and in-traplatelet organic matrix can be both decomposed by sodium hydroxide solution,the chemical stability of individual aragonite platelets is much higher than that of the microstructure stacked with them. Further,macroscopic bending test or nanoindentation experiment is performed on the micro/nanostructure of nacre after sodium hydroxide treatment. It is found that the Young’s modulus of both the stacked microstructure and nanocomposite platelet reduced. The reduction of the microstructure is more remark than that of the platelet. Therefore the chemical-mechanical stability of the nanocomposite platelet itself is much higher than that of the stacked microstructure of nacre.

  16. Genotoxic hazards of azo pigments and other colorants related to 1-phenylazo-2-hydroxynaphthalene.

    Science.gov (United States)

    Møller, P; Wallin, H

    2000-01-01

    Azo pigments are used extensively as coloring agents in inks, paints and cosmetics. We have surveyed the literature for genotoxic and cancer data on nine colorants, which are structurally related to 1-phenylazo-2-hydroxynaphthalene (C.I. Solvent yellow 14). C.I. Solvent yellow 14 is metabolized by oxidative and peroxidative enzymes. Metabolically activated C.I. Solvent yellow 14 forms both RNA and DNA adducts. It induces liver nodules in rats upon oral administration. Although there is a mixture of negative and positive findings in short-term tests and in animal cancer studies, C.I. Solvent yellow 14 should be considered genotoxic. C.I. Pigment red 3 should be considered carcinogenic but is only weakly genotoxic. C.I. Solvent yellow 7, C.I. Pigment orange 5, C.I. Pigment red 4, and C.I. Pigment red 23 should be considered genotoxic. C.I. Pigment red 53:1 is not genotoxic, and observations of spleen tumors in male rats but not in female rats or mice seem to be related to toxic effects of high doses of C.I. Pigment red 53:1 in this organ. The data in the literature indicate that Pigment red 57:1 is not genotoxic or carcinogenic. We did not find sufficient data for a relevant evaluation of C.I. Pigment red 2 and C.I. Pigment red 64:1. Some of the colorants have in common the 2-amino-1-naphthol structure. This compound is not genotoxic. On the other hand, reductive cleavage of the azo bonds or hydrolysis of anilido bonds would produce aromatic amines, most of which have been under suspicion for genotoxicity or carcinogenicity. For C.I. Pigment red 53:1 and 57:1, sulphonated aromatic amines would be formed that are not genotoxic.

  17. An R2R3-MYB transcription factor regulates carotenoid pigmentation in Mimulus lewisii flowers.

    Science.gov (United States)

    Sagawa, Janelle M; Stanley, Lauren E; LaFountain, Amy M; Frank, Harry A; Liu, Chang; Yuan, Yao-Wu

    2016-02-01

    Carotenoids are yellow, orange, and red pigments that contribute to the beautiful colors and nutritive value of many flowers and fruits. The structural genes in the highly conserved carotenoid biosynthetic pathway have been well characterized in multiple plant systems, but little is known about the transcription factors that control the expression of these structural genes. By analyzing a chemically induced mutant of Mimulus lewisii through bulk segregant analysis and transgenic experiments, we have identified an R2R3-MYB, Reduced Carotenoid Pigmentation 1 (RCP1), as the first transcription factor that positively regulates carotenoid biosynthesis during flower development. Loss-of-function mutations in RCP1 lead to down-regulation of all carotenoid biosynthetic genes and reduced carotenoid content in M. lewisii flowers, a phenotype recapitulated by RNA interference in the wild-type background. Overexpression of this gene in the rcp1 mutant background restores carotenoid production and, unexpectedly, results in simultaneous decrease of anthocyanin production in some transgenic lines by down-regulating the expression of an activator of anthocyanin biosynthesis. Identification of transcriptional regulators of carotenoid biosynthesis provides the 'toolbox' genes for understanding the molecular basis of flower color diversification in nature and for potential enhancement of carotenoid production in crop plants via genetic engineering. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  18. Light-driven oxidation of polysaccharides by photosynthetic pigments and a metalloenzyme

    DEFF Research Database (Denmark)

    Cannella, David; Möllers, K. Benedikt; Frigaard, Niels-Ulrik

    2016-01-01

    the effect of using excited photosynthetic pigments as electron donors. LPMOs combined with pigments and reducing agents were exposed to light, which resulted in a never before seen 100-fold increase in catalytic activity. In addition, LPMO substrate specificity was broadened to include both cellulose...... and hemicellulose. LPMO enzymes and pigment derivatives common in the environment of plant-degrading organisms thus form a highly reactive and stable light-driven system increasing the turnover rate and versatility of LPMOs. This light-driven system may find applications in biotechnology and chemical processing....

  19. PACSY, a relational database management system for protein structure and chemical shift analysis.

    Science.gov (United States)

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  20. Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

    Science.gov (United States)

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

  1. Structural and Optical Properties of Chemical Bath Deposited Silver Oxide Thin Films: Role of Deposition Time

    Directory of Open Access Journals (Sweden)

    A. C. Nwanya

    2013-01-01

    Full Text Available Silver oxide thin films were deposited on glass substrates at a temperature of 50°C by chemical bath deposition technique under different deposition times using pure AgNO3 precursor and triethanolamine as the complexing agent. The chemical analysis based on EDX technique shows the presence of Ag and O at the appropriate energy levels. The morphological features obtained from SEM showed that the AgxO structures varied as the deposition time changes. The X-ray diffraction showed the peaks of Ag2O and AgO in the structure. The direct band gap and the refractive index increased as the deposition time increased and was in the range of 1.64–1.95 eV and 1.02–2.07, respectively. The values of the band gap and refractive index obtained indicate possible applications in photovoltaic and photothermal systems.

  2. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.

    Science.gov (United States)

    Leitner, Alexander; Walzthoeni, Thomas; Kahraman, Abdullah; Herzog, Franz; Rinner, Oliver; Beck, Martin; Aebersold, Ruedi

    2010-08-01

    Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to provide important information about native protein structure and the topology of protein complexes. In this article, we discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of cross-linking data for computational modeling. Finally, the impact of protein cross-linking on various biological disciplines is highlighted.

  3. Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.

    Directory of Open Access Journals (Sweden)

    Olga Tatarinova

    Full Text Available Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.

  4. Pigmentation in sand pear (Pyrus pyrifolia) fruit: biochemical characterization, gene discovery and expression analysis with exocarp pigmentation mutant.

    Science.gov (United States)

    Wang, Yue-zhi; Zhang, Shujun; Dai, Mei-song; Shi, Ze-bin

    2014-05-01

    Exocarp color of sand pear is an important trait for the fruit production and has caused our concern for a long time. Our previous study explored the different expression genes between the two genotypes contrasting for exocarp color, which indicated the different suberin, cutin, wax and lignin biosynthesis between the russet- and green-exocarp. In this study, we carried out microscopic observation and Fourier transform infrared spectroscopy analysis to detect the differences of tissue structure and biochemical composition between the russet- and green-exocarp of sand pear. The green exocarp was covered with epidermis and cuticle which was replaced by a cork layer on the surface of russet exocarp, and the chemicals of the russet exocarp were characterized by lignin, cellulose and hemicellulose. We explored differential gene expression between the russet exocarp of 'Niitaka' and its green exocarp mutant cv. 'Suisho' using Illumina RNA-sequencing. A total of 559 unigenes showed different expression between the two types of exocarp, and 123 of them were common to the previous study. The quantitative real time-PCR analysis supports the RNA-seq-derived gene with different expression between the two types of exocarp and revealed the preferential expression of these genes in exocarp than in mesocarp and fruit core. Gene ontology enrichment analysis revealed divorced expression of lipid metabolic process genes, transport genes, stress responsive genes and other biological process genes in the two types of exocarp. Expression changes in lignin metabolism-related genes were consistent with the different pigmentation of russet and green exocarp. Increased transcripts of putative genes involved the suberin, cutin and wax biosynthesis in 'Suisho' exocarp could facilitate deposition of the chemicals and take a role in the mutant trait responsible for the green exocarp. In addition, the divorced expression of ATP-binding cassette transporters involved in the trans

  5. Hybrid pigment organelles in an invertebrate.

    Science.gov (United States)

    Schliwa, M; Euteneuer, U

    1979-02-28

    Observations of a number of vertebrate chromatophores have revealed the presence of more than one type of pigment organelles, suggesting that the different types are all derived from an equipotential organelle able to differentiate into any of the major pigment-containing organelles (Bagnara, 1972). Observations are presented concerning the occurrence of hybrid pigment inclusions, i.e., all kinds of intergrades between melanosomes, pterinosomes, and reflecting platelets in pigment cells of the daddy-long-legs. It therefore seems possible that pigment organelles in some invertebrates may also be derived from a common pluripotential primordial organelle.

  6. Processing of poly(lactic acid): characterization of chemical structure, thermal stability and mechanical properties

    OpenAIRE

    Carrasco Alonso, Félix Ángel; Pagès Figueras, Pere; Gamez Pérez, José; Santana Pérez, Orlando Onofre; Maspoch Rulduà, Mª Lluïsa

    2010-01-01

    The processing of poly(lactic acid) (injection and extrusion/injection) as well as annealing of processed materials were studied in order to analyze the variation of its chemical structure, thermal degradation and mechanical properties. Processing of PLA was responsible for a decrease in molecular weight, as determined by GPC, due to chain scission. The degree of crystallinity was evaluated by means of differential scanning calorimetry and X-ray diffraction. It was found that mech...

  7. Chemical descriptors, convexity and structure of density matrices in molecular systems

    CERN Document Server

    Bochicchio, Roberto C

    2015-01-01

    The electron energy and density matrices in molecular systems are convex in respect of the number of particles. So that, the chemical descriptors based on their derivatives present the hamper of discontinuities for isolated systems and consequently higher order derivatives are undefined. The introduction of the interaction between the physical domain with an environment induces a coherent structure for the density matrix in the grand-canonical formulation suppressing the discontinuities leading to the proper definitions of the descriptors.

  8. Structural, optical and electrical properties of chemically deposited nonstoichiometric copper indium diselenide films

    Indian Academy of Sciences (India)

    R H Bari; L A Patil; P P Patil

    2006-10-01

    Thin films of copper indium diselenide (CIS) were prepared by chemical bath deposition technique onto glass substrate at temperature, 60°C. The studies on composition, morphology, optical absorption, electrical conductivity and structure of the films were carried out and discussed. Characterization included X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), energy dispersive X-ray analysis (EDAX) and absorption spectroscopy. The results are discussed and interpreted.

  9. Physico-chemical properties and cytotoxic effects of sugar-based surfactants: Impact of structural variations.

    Science.gov (United States)

    Lu, Biao; Vayssade, Muriel; Miao, Yong; Chagnault, Vincent; Grand, Eric; Wadouachi, Anne; Postel, Denis; Drelich, Audrey; Egles, Christophe; Pezron, Isabelle

    2016-09-01

    Surfactants derived from the biorefinery process can present interesting surface-active properties, low cytotoxicity, high biocompatibility and biodegradability. They are therefore considered as potential sustainable substitutes to currently used petroleum-based surfactants. To better understand and anticipate their performances, structure-property relationships need to be carefully investigated. For this reason, we applied a multidisciplinary approach to systematically explore the effect of subtle structural variations on both physico-chemical properties and biological effects. Four sugar-based surfactants, each with an eight carbon alkyl chain bound to a glucose or maltose head group by an amide linkage, were synthesized and evaluated together along with two commercially available standard surfactants. Physico-chemical properties including solubility, Krafft point, surface-tension lowering and critical micellar concentration (CMC) in water and biological medium were explored. Cytotoxicity evaluation by measuring proliferation index and metabolic activity against dermal fibroblasts showed that all surfactants studied may induce cell death at low concentrations (below their CMC). Results revealed significant differences in both physico-chemical properties and cytotoxic effects depending on molecule structural features, such as the position of the linkage on the sugar head-group, or the orientation of the amide linkage. Furthermore, the cytotoxic response increased with the reduction of surfactant CMC. This study underscores the relevance of a methodical and multidisciplinary approach that enables the consideration of surfactant solution properties when applied to biological materials. Overall, our results will contribute to a better understanding of the concomitant impact of surfactant structure at physico-chemical and biological levels.

  10. Relationship between the antitrichinellous effect of seven derivates of benzimidazolecarbamates and their chemical structure.

    Science.gov (United States)

    Spaldonová, R; Corba, J

    1979-01-01

    The efficacy of seven more recently developed anthelmintics of the benzimidazolecarbamate group, i. e., parbendazole, mebendazole, fenbendazole, oxibendazole, cambendazole, oxfendazole and albendazole, has been tested in a series of experiments on white mice artifically infected with Trichinella spiralis. Our results disclosed a relationship between their anthelmintic effect and their chemical structure. This finding might be of importance in a targeted synthesis of new, effective, derivates of benzimidazole, e. g., in the therapy of trichinellosis and in the choice of the most effective drug.

  11. Chemical structure of the O-polysaccharide isolated from Pectobacterium atrosepticum SCRI 1039.

    Science.gov (United States)

    Czerwicka, Małgorzata; Marszewska, Kinga; Bychowska, Anna; Dziadziuszko, Halina; Brzozowski, Krzysztof; Łojkowska, Ewa; Stepnowski, Piotr; Kaczyński, Zbigniew

    2011-12-27

    The lipopolysaccharide (LPS) of the bacterium Pectobacterium atrosepticum SCRI 1039 was hydrolyzed and the products were separated. A study of the obtained O-polysaccharide by means of chemical methods, GLC, GLC-MS, and NMR spectroscopy allowed us to identify a branched polymer with a pentasaccharide repeating unit of the structure shown below, in which the fucose residue was partially O-acetylated at C-2, C-3 or C-4.

  12. Analysis of the relationship between the structure and aromatic properties of chemical compounds.

    Science.gov (United States)

    Debska, Barbara; Guzowska-Swider, Barbara

    2003-04-01

    This paper presents the results of research on the relationship between the structure and odour properties of a selection of chemical compounds. The research concerns five groups of esters, each with a different smell: almond, apricot, apple, pineapple and rose. The supposed relationship between the smell and certain selected attributes of each molecule was examined by various pattern recognition techniques using programs developed in the Department of Computer Chemistry at Rzeszów University of Technology.

  13. Chemically gated electronic structure of a superconducting doped topological insulator system

    Science.gov (United States)

    Wray, L. A.; Xu, S.; Neupane, M.; Fedorov, A. V.; Hor, Y. S.; Cava, R. J.; Hasan, M. Z.

    2013-07-01

    Angle resolved photoemission spectroscopy is used to observe changes in the electronic structure of bulk-doped topological insulator CuxBi2Se3 as additional copper atoms are deposited onto the cleaved crystal surface. Carrier density and surface-normal electrical field strength near the crystal surface are estimated to consider the effect of chemical surface gating on atypical superconducting properties associated with topological insulator order, such as the dynamics of theoretically predicted Majorana Fermion vortices.

  14. Clay pigment structure characterisation as a guide for provenance determination--a comparison between laboratory powder micro-XRD and synchrotron radiation XRD.

    Science.gov (United States)

    Švarcová, Silvie; Bezdička, Petr; Hradil, David; Hradilová, Janka; Žižak, Ivo

    2011-01-01

    Application of X-ray diffraction (XRD)-based techniques in the analysis of painted artworks is not only beneficial for indisputable identification of crystal constituents in colour layers, but it can also bring insight in material crystal structure, which can be affected by their geological formation, manufacturing procedure or secondary changes. This knowledge might be helpful for art historic evaluation of an artwork as well as for its conservation. By way of example of kaolinite, we show that classification of its crystal structure order based on XRD data is useful for estimation of its provenance. We found kaolinite in the preparation layer of a Gothic wall painting in a Czech church situated near Karlovy Vary, where there are important kaolin deposits. Comparing reference kaolin materials from eight various Czech deposits, we found that these can be differentiated just according to the kaolinite crystallinity. Within this study, we compared laboratory powder X-ray micro-diffraction (micro-XRD) with synchrotron radiation X-ray diffraction analysing the same real sample. We found that both techniques led to the same results.

  15. Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Rekha, E-mail: rekha.mittal07@gmail.com; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K. [Thin Film Laboratory, Physics Department, Indian Institute of Technology Delhi, New Delhi-110016 (India)

    2016-05-06

    Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.

  16. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis.

    Science.gov (United States)

    Suyama, Takashi L; Gerwick, William H; McPhail, Kerry L

    2011-11-15

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

  17. Chemically defined structured lipids: current status and future directions in gastrointestinal diseases.

    Science.gov (United States)

    Stein, J

    1999-04-01

    Over the past two decades various concepts for the supply of lipids in parenteral and enteral nutrition have been developed. Traditionally, the nutritional dietary management typically includes physical mixtures of medium chain and long-chain triglycerides. Recently, chemically defined structured lipids have been developed that combine the advantages of conventional fats with those of special purposes. The first structured lipids were produced by mixing pure medium-chain triglycerides and long-chain triglycerides, allowing hydrolysis to free fatty acids, followed by random transesterification of the fatty acids into mixed triglyceride molecules. This results in a triglyceride containing combinations of short-, medium-, and long-chain fatty acids on a single glycerol backbone. These have unique chemical, physical, and/or physiological properties which differ from simply blending mixtures from the starting fats. By use of 1,3-specific or 2-specific lipases it is now possible to synthesize 1,3-specific or 2-specific triglycerides containing short- and/or medium-chain acids. For instance, incorporation of linoleic, arachidonic, or eicosapentaenoic acid at the sn-2 position is being evaluated for the specific objective of modulating membrane fatty acid composition and essential fatty acid absorption in models of cancer, burns, and immune dysfunction. This contribution reviews the current status of experimental and clinical studies of chemically defined structured lipid-based fat emulsions, with emphasis on their therapeutic potential for nutritional support in hospitalized patients.

  18. Improved performance of the microbial electrolysis desalination and chemical-production cell using the stack structure.

    Science.gov (United States)

    Chen, Shanshan; Liu, Guangli; Zhang, Renduo; Qin, Bangyu; Luo, Yong; Hou, Yanping

    2012-07-01

    The microbial electrolysis desalination and chemical-production cell (MEDCC) is a device to desalinate seawater, and produce acid and alkali. The objective of this study was to enhance the desalination and chemical-production performance of the MEDCC using two types of stack structure. Experiments were conducted with different membrane spacings, numbers of desalination chambers and applied voltages. Results showed that the stack construction in the MEDCC enhanced the desalination and chemical-production rates. The maximal desalination rate of 0.58 ± 0.02 mmol/h, which was 43% higher than that in the MEDCC, was achieved in the four-desalination-chamber MEDCC with the AEM-CEM stack structure and the membrane spacing of 1.5mm. The maximal acid- and alkali-production rates of 0.079 ± 0.006 and 0.13 ± 0.02 mmol/h, which were 46% and 8% higher than that in the MEDCC, respectively, were achieved in the two-desalination-chamber MEDCC with the BPM-AEM-CEM stack structure and the membrane spacing of 3mm.

  19. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  20. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  1. Damascene Array Structure of Phase Change Memory Fabricated with Chemical Mechanical Polishing Method

    Institute of Scientific and Technical Information of China (English)

    LIU Qi-Bin; SONG Zhi-Tang; ZHANG Kai-Liang; WANG Liang-Yong; FENG Song-Lin; CHEN Bomy

    2006-01-01

    @@ A damascene structure of phase change memory (PCM) is fabricated successfully with the chemical mechanical polishing (CMP) method, and the CMP of Ge2Sb2Te5 (GST) and Ti films is investigated. The polished surface of wafer is analysed by scanning electron microscopy (SEM) and an energy dispersive spectrometer (EDS). The measurements show that the damascene device structure of phase change memory is achieved by the CMP process.After the top electrode is deposited, dc sweeping test on PCM reveals that the phase change can be observed.The threshold current of array cells varies between 0.90mA and 1.15mA.

  2. Chemical structure of asphaltenes of tar semicoked from Kansk-Achinsk lignite

    Energy Technology Data Exchange (ETDEWEB)

    Platanov, V.V.; Proskuryakov, V.A.; Klyavina, O.A. [Ln Tolstoi Tula State Pedagogical Institute, Tula (Russian Federation)

    1994-03-01

    The chemical structure has been studied of asphaltenes of tar semicoked from Kansk-Achinsk lignite and recovered at a temperature less than or equal to 350{degree}C. Asphaltenes have been found to be a complete mixture of aromatic, alicyclic, hydroaromatic, and heterocyclic compounds substituted by alkyl chains and various functional groups. A number of asphaltene compounds originate from steroids and triterpanes, which widely occur in lipid and tar fractions of plants and in the metabolites of microbes. A procedure based on adsorptive liquid chromatography has been developed to separate asphaltenes into a great number of eluates with considerably differing structural parameters and functional compositions.

  3. Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks.

    Science.gov (United States)

    Bernazzani, Luca; Duce, Celia; Micheli, Alessio; Mollica, Vincenzo; Sperduti, Alessandro; Starita, Antonina; Tiné, Maria Rosaria

    2006-01-01

    In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, Delta(solv)G degrees , has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the Delta(solv)G degrees in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R = 0.9985, standard deviation S = 0.68 kJ mol(-1), and mean absolute error MAE = 0.46 kJ mol(-1). The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the

  4. Electronic structure and chemical bonding of Li4Pt3Si

    Science.gov (United States)

    Matar, S. F.; Pöttgen, R.; Al Alam, A. F.; Ouaini, N.

    2012-07-01

    The electronic structure of rhombohedral Li4Pt3Si (space group R32) is examined from ab initio with an assessment of the properties of chemical bonding relating to the presence of different Li and Pt Wyckoff sites. The structure with totally de-intercalated Li keeps the characteristics of the pristine compound with a reduction of the volume albeit with less cohesive energy. The binding energies of Li point to different bonding intensities according to their different Wyckoff sites and indicate the possibility of delithiation.

  5. Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James; Freeland, Stephen J

    2013-11-25

    α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

  6. Preparation of melanin from Catharsius molossus L. and preliminary study on its chemical structure.

    Science.gov (United States)

    Xin, Chao; Ma, Jia-hua; Tan, Cheng-jia; Yang, Zhou; Ye, Feng; Long, Chan; Ye, Shuang; Hou, Da-bin

    2015-04-01

    A great deal of melanin was found in the waste alkali liquor produced by extraction of chitin from Catharsius molossus L. Discarding the lye could harm the environment and cause waste of resources. In this paper, melanin from C. molossus L. was recovered through acid precipitation and purified by pepsin and so on. The purity, chemical composition and structure of the prepared melanin were explored by UV-visible absorption spectroscopy, Fourier transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, high resolution (13)C Cross polarization magic angle spinning nuclear magnetic resonance spectroscopy pyrolysis gas chromatography mass spectrometry, X ray diffraction, X ray fluorescence, matrix-assisted laser desorption/ionization time of flight tandem mass spectrometry, thermal analysis, and so on. The results showed that the purity of the prepared melanin was higher than the commercial standard melanin and it was a kind of nanoaggregates composed of a large quantity of 5,6-dihydroxyindole eumelanin and a small amount of phaeomelanin. In addition, the prepared melanin was irregular in shape and its structure could be divided into three levels: advanced structure maintained by polypeptides, substructure maintained by the ferric ion and microstructure. In particular, the smallest structural unit showed the graphite-like layered structure containing five layers linked by non-covalent bonds and each layer mainly consisted of 5,6-dihydroxyindole and its derivatives, which might be connected to each other through various chemical bonds.

  7. Availability and Utilization of Pigments from Microalgae.

    Science.gov (United States)

    Begum, Hasina; Yusoff, Fatimah Md; Banerjee, Sanjoy; Khatoon, Helena; Shariff, Mohamed

    2016-10-02

    Microalgae are the major photosynthesizers on earth and produce important pigments that include chlorophyll a, b and c, β-carotene, astaxanthin, xanthophylls, and phycobiliproteins. Presently, synthetic colorants are used in food, cosmetic, nutraceutical, and pharmaceutical industries. However, due to problems associated with the harmful effects of synthetic colorants, exploitation of microalgal pigments as a source of natural colors becomes an attractive option. There are various factors such as nutrient availability, salinity, pH, temperature, light wavelength, and light intensity that affect pigment production in microalgae. This paper reviews the availability and characteristics of microalgal pigments, factors affecting pigment production, and the application of pigments produced from microalgae. The potential of microalgal pigments as a source of natural colors is enormous as an alternative to synthetic coloring agents, which has limited applications due to regulatory practice for health reasons.

  8. Skin pigmentation kinetics after UVB exposure

    DEFF Research Database (Denmark)

    Ravnbak, M.H.; Philipsen, P.A.; Wiegell, S.R.

    2008-01-01

    There have been few previous studies of the kinetics of pigmentation following ultraviolet B (UVB) exposure, and these have included only fair-skinned persons. The current study investigated pigmentation increase to steady state and fading in 12 Scandinavians and 12 Indians/Pakistanis. Over...... a period of 3 weeks the subjects were UV-irradiated 6 times on the right side of the back and 12 times on the left side using a Solar Simulator and narrowband UVB with equal sub-Minimal Melanogenesis Doses (individually predetermined). Pigmentation was measured from skin remittance at 555 urn and 660 nm...... (allowing correction for erythema). The absolute pigmentation increase was independent of pre-exposure pigmentation, therefore the percentage pigmentation increase was higher in fair-skinned volunteers. The UV dose to minimal pigmentation was higher in darker-skinned persons for single and multiple UV...

  9. A Photoluminescence Study of the Changes Induced in the Zinc White Pigment by Formation of Zinc Complexes.

    Science.gov (United States)

    Artesani, Alessia; Gherardi, Francesca; Nevin, Austin; Valentini, Gianluca; Comelli, Daniela

    2017-03-25

    It is known that oil paintings containing zinc white are subject to rapid degradation. This is caused by the interaction between the active groups of binder and the metal ions of the pigment, which gives rise to the formation of new zinc complexes (metal soaps). Ongoing studies on zinc white paints have been limited to the chemical mechanisms that lead to the formation of zinc complexes. On the contrary, little is known of the photo-physical changes induced in the zinc oxide crystal structure following this interaction. Time-resolved photoluminescence spectroscopy has been applied to follow modifications in the luminescent zinc white pigment when mixed with binder. Significant changes in trap state photoluminescence emissions have been detected: the enhancement of a blue emission combined with a change of the decay kinetic of the well-known green emission. Complementary data from molecular analysis of paints using Fourier transform infrared spectroscopy confirms the formation of zinc carboxylates and corroborates the mechanism for zinc complexes formation. We support the hypothesis that zinc ions migrate into binder creating novel vacancies, affecting the photoluminescence intensity and lifetime properties of zinc oxide. Here, we further demonstrate the advantages of a time-resolved photoluminescence approach for studying defects in semiconductor pigments.

  10. Changes in the chemical structure of polytetrafluoroethylene induced by electron beam irradiation in the molten state

    CERN Document Server

    Lappan, U; Lunkwitz, K

    2000-01-01

    Polytetrafluoroethylene (PTFE) was exposed to electron beam radiation at elevated temperature above the melting point under nitrogen atmosphere and in vacuum for comparison. Fourier-transform infrared (FTIR) spectroscopy was used to study the changes in the chemical structure. The irradiation under nitrogen atmosphere leads to the same structures as described recently for PTFE irradiated in vacuum. Trifluoromethyl branches and double bond structures were detected. The concentrations of terminal and internal double bonds are higher after irradiation under nitrogen than in vacuum. Annealing experiments have shown that the thermal oxidative stability of the radiation-modified PTFE is reduced compared to unirradiated PTFE. The reason are the formation of unstable structures such as double bonds.

  11. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology.

    Science.gov (United States)

    Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

    2015-08-01

    Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.

  12. Crystal engineering on industrial diaryl pigments using lattice energy minimizations and X-ray powder diffraction.

    Science.gov (United States)

    Schmidt, Martin U; Dinnebier, Robert E; Kalkhof, Holger

    2007-08-23

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  13. Crystal Engineering on Industrial Diaryl Pigments Using Lattice Energy Minimizations and X-ray Powder Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt,M.; Dinnebier, R.; Kalkhof, H.

    2007-01-01

    Diaryl azo pigments play an important role as yellow pigments for printing inks, with an annual pigment production of more than 50,000 t. The crystal structures of Pigment Yellow 12 (PY12), Pigment Yellow 13 (PY13), Pigment Yellow 14 (PY14), and Pigment Yellow 83 (PY83) were determined from X-ray powder data using lattice energy minimizations and subsequent Rietveld refinements. Details of the lattice energy minimization procedure and of the development of a torsion potential for the biphenyl fragment are given. The Rietveld refinements were carried out using rigid bodies, or constraints. It was also possible to refine all atomic positions individually without any constraint or restraint, even for PY12 having 44 independent non-hydrogen atoms per asymmetric unit. For PY14 (23 independent non-hydrogen atoms), additionally all atomic isotropic temperature factors could be refined individually. PY12 crystallized in a herringbone arrangement with twisted biaryl fragments. PY13 and PY14 formed a layer structure of planar molecules. PY83 showed a herringbone structure with planar molecules. According to quantum mechanical calculations, the twisting of the biaryl fragment results in a lower color strength of the pigments, whereas changes in the substitution pattern have almost no influence on the color strength of a single molecule. Hence, the experimentally observed lower color strength of PY12 in comparison with that of PY13 and PY83 can be explained as a pure packing effect. Further lattice energy calculations explained that the four investigated pigments crystallize in three different structures because these structures are the energetically most favorable ones for each compound. For example, for PY13, PY14, or PY83, a PY12-analogous crystal structure would lead to considerably poorer lattice energies and lower densities. In contrast, lattice energy calculations revealed that PY12 could adopt a PY13-type structure with only slightly poorer energy. This structure was

  14. Pigment identification in pictorial layers by HyperSpectral Imaging

    Science.gov (United States)

    Capobianco, Giuseppe; Bonifazi, Giuseppe; Prestileo, Fernanda; Serranti, Silvia

    2014-05-01

    The use of Hyper-Spectral Imaging (HSI) as a diagnostic tool in the field of cultural heritage is of great interest presenting high potentialities. This analysis, in fact, is non-destructive, non-invasive and portable. Furthermore, the possibility to couple hyperspectral data with chemometric techniques allows getting qualitative and/or quantitative information on the nature and physical-chemical characteristics of the investigated materials. A study was carried out to explore the possibilities offered by this approach to identify pigments in paintings. More in detail, six pigments have been selected and they have been then mixed with four different binders and applied to a wood support. The resulting reference samples were acquired by HSI in the SWIR wavelength range (1000-2500 nm). Data were processed adopting a chemometric approach based on the PLS Toolbox (Eigenvector Research, Inc.) running inside Matlab® (The Mathworks, Inc.). The aim of the study was to verify, according to the information acquired in the investigated wavelength region, the correlation existing between collected spectral signatures and sample characteristics related to the different selected pigments and binders. Results were very good showing as correlations exist. New scenarios can thus be envisaged for analysis, characterization, conservation and restoration of paintings, considering that the developed approach allows to obtain, just "in one shot", information, not only on the type of pigment, but also on the utilized binder and support.

  15. Photoinduced changes in photosystem II pigments

    Science.gov (United States)

    Andreeva, Atanaska S.; Busheva, Mira C.; Stoitchkova, Katerina V.; Tzonova, Iren K.

    2010-11-01

    The photosynthetic apparatus in higher plants performs two seemingly opposing tasks: efficient harvest of sunlight, but also rapid and harmless dissipation of excess light energy as heat to avoid deleterious photodamage. In order to study this process in pigment-protein supercomplexes of photosystem II (PSII), 77 K fluorescence and room temperature resonance Raman (RR) spectroscopy were applied to investigate the changes in structure and spectral properties of the pigments in spinach PSII membranes. The high-light treatment results in a strong quenching of the fluorescence (being largest when the excitation is absorbed by carotenoids) and a red-shift of the main maximum. Decomposition of the fluorescence spectra into four bands revealed intensive quenching of F685 and F695 bands, possible bleaching of chlorophyll a, enhanced extent of light harvesting complexes (LHCII) aggregation and increased energy transfer to aggregated LHCII. The analysis of RR spectra revealed the predominant contribution of ß-carotene (ß-Car) upon 457.8 and 488 nm excitations and lutein (Lut) at 514.5 nm. During prolonged exposure to strong light no significant bleaching of ß-Car and weak photobleaching of Lut is observed. The results will contribute to the efforts to produce more efficient and robust solar cells when exposed to fluctuations in light intensity.

  16. Drying of Pigment-Cellulose Nanofibril Substrates

    Directory of Open Access Journals (Sweden)

    Oleg Timofeev

    2014-10-01

    Full Text Available A new substrate containing cellulose nanofibrils and inorganic pigment particles has been developed for printed electronics applications. The studied composite structure contains 80% fillers and is mechanically stable and flexible. Before drying, the solids content can be as low as 20% due to the high water binding capacity of the cellulose nanofibrils. We have studied several drying methods and their effects on the substrate properties. The aim is to achieve a tight, smooth surface keeping the drying efficiency simultaneously at a high level. The methods studied include: (1 drying on a hot metal surface; (2 air impingement drying; and (3 hot pressing. Somewhat surprisingly, drying rates measured for the pigment-cellulose nanofibril substrates were quite similar to those for the reference board sheets. Very high dewatering rates were observed for the hot pressing at high moisture contents. The drying method had significant effects on the final substrate properties, especially on short-range surface smoothness. The best smoothness was obtained with a combination of impingement and contact drying. The mechanical properties of the sheets were also affected by the drying method and associated temperature.

  17. Structuring of DLC:Ag nanocomposite thin films employing plasma chemical etching and ion sputtering

    Science.gov (United States)

    Tamulevičius, Tomas; Tamulevičienė, Asta; Virganavičius, Dainius; Vasiliauskas, Andrius; Kopustinskas, Vitoldas; Meškinis, Šarūnas; Tamulevičius, Sigitas

    2014-12-01

    We analyze structuring effects of diamond like carbon based silver nanocomposite (DLC:Ag) thin films by CF4/O2 plasma chemical etching and Ar+ sputtering. DLC:Ag films were deposited employing unbalanced reactive magnetron sputtering of silver target with Ar+ in C2H2 gas atmosphere. Films with different silver content (0.6-12.9 at.%) were analyzed. The films (as deposited and exposed to plasma chemical etching) were characterized employing scanning electron microscopy and energy dispersive X-ray analysis (SEM/EDS), optical microscopy, ultraviolet-visible light (UV-VIS) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. After deposition, the films were plasma chemically etched in CF4/O2 mixture plasma for 2-6 min. It is shown that optical properties of thin films and silver nano particle size distribution can be tailored during deposition changing the magnetron current and C2H2/Ar ratio or during following plasma chemical etching. The plasma etching enabled to reveal the silver filler particle size distribution and to control silver content on the surface that was found to be dependent on Ostwald ripening process of silver nano-clusters. Employing contact lithography and 4 μm period mask in photoresist or aluminum the films were patterned employing CF4/O2 mixture plasma chemical etching, direct Ar+ sputtering or combined etching processes. It is shown that different processing recipes result in different final grating structures. Selective carbon etching in CF4/O2 gas mixture with photoresist mask revealed micrometer range lines of silver nanoparticles, while Ar+ sputtering and combined processing employing aluminum mask resulted in nanocomposite material (DLC:Ag) micropatterns.

  18. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Science.gov (United States)

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  19. Integrating Epistemological Perspectives on Chemistry in Chemical Education: The Cases of Concept Duality, Chemical Language, and Structural Explanations

    Science.gov (United States)

    Kaya, Ebru; Erduran, Sibel

    2013-01-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ("Foundations of Chemistry"…

  20. Chemical engineering and structural and pharmacological characterization of the α-scorpion toxin OD1.

    Science.gov (United States)

    Durek, Thomas; Vetter, Irina; Wang, Ching-I Anderson; Motin, Leonid; Knapp, Oliver; Adams, David J; Lewis, Richard J; Alewood, Paul F

    2013-01-01

    Scorpion α-toxins are invaluable pharmacological tools for studying voltage-gated sodium channels, but few structure-function studies have been undertaken due to their challenging synthesis. To address this deficiency, we report a chemical engineering strategy based upon native chemical ligation. The chemical synthesis of α-toxin OD1 was achieved by chemical ligation of three unprotected peptide segments. A high resolution X-ray structure (1.8 Å) of synthetic OD1 showed the typical βαββ α-toxin fold and revealed important conformational differences in the pharmacophore region when compared with other α-toxin structures. Pharmacological analysis of synthetic OD1 revealed potent α-toxin activity (inhibition of fast inactivation) at Nav1.7, as well as Nav1.4 and Nav1.6. In addition, OD1 also produced potent β-toxin activity at Nav1.4 and Nav1.6 (shift of channel activation in the hyperpolarizing direction), indicating that OD1 might interact at more than one site with Nav1.4 and Nav1.6. Investigation of nine OD1 mutants revealed that three residues in the reverse turn contributed significantly to selectivity, with the triple OD1 mutant (D9K, D10P, K11H) being 40-fold more selective for Nav1.7 over Nav1.6, while OD1 K11V was 5-fold more selective for Nav1.6 than Nav1.7. This switch in selectivity highlights the importance of the reverse turn for engineering α-toxins with altered selectivity at Nav subtypes.

  1. Pigmented villonodular synovitis: MRI characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Hughes, T.H. [Dept. of Radiology, Univ. of California, San Diego, CA (United States)]|[Veterans Administration Medical Center, San Diego, CA (United States); Sartoris, D.J. [Dept. of Radiology, Univ. of California, San Diego, CA (United States)]|[Veterans Administration Medical Center, San Diego, CA (United States); Schweitzer, M.E. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Resnick, D.L. [Dept. of Radiology, Univ. of California, San Diego, CA (United States)]|[Veterans Administration Medical Center, San Diego, CA (United States)

    1995-01-01

    The magnetic resonance imaging (MRI) scans of 26 patients with histopathologically proven pigmented villonodular synovitis (PVNS), involving joints but excluding tendon sheaths, were reviewed retrospectively. The purpose of this study is to define the spectrum and frequency of MRI characteristics for PVNS using conventional spin echo (in two cases before and after intravenous administration of gadopentate dimeglumine) and also gradient echo techniques. A cystic variety is presented, the MRI appearances of which have not been found in a review of the literature. (orig.)

  2. Nanoscience of an ancient pigment.

    Science.gov (United States)

    Johnson-McDaniel, Darrah; Barrett, Christopher A; Sharafi, Asma; Salguero, Tina T

    2013-02-06

    We describe monolayer nanosheets of calcium copper tetrasilicate, CaCuSi(4)O(10), which have strong near-IR luminescence and are amenable to solution processing methods. The facile exfoliation of bulk CaCuSi(4)O(10) into nanosheets is especially surprising in view of the long history of this material as the colored component of Egyptian blue, a well-known pigment from ancient times.

  3. Dynamics of phytoplankton pigments in water and surface sediments of a large shallow lake

    Directory of Open Access Journals (Sweden)

    Ilmar Tõnno

    2011-06-01

    Full Text Available Our aim was to find out to which extent fossil phytoplankton pigments in the large shallow and turbid Lake Võrtsjärv carry information on the history of phytoplankton communities. For this purpose we examined how the changes in the pigment composition of surface sediments follow their changes in the water column. Depth-integrated lake water and surface sediment samples were collected weekly in May–October 2007. Considering cyanobacterial and diatom dominance in phytoplankton, we analysed fucoxanthin, diadinoxanthin and diatoxanthin as marker pigments for diatoms, zeaxanthin as a marker pigment for total cyanobacteria and canthaxanthin as a marker pigment for colonial cyanobacteria. Chlorophyll a and its derivative pheophytin a were applied as indicators for total phytoplankton. The dynamics of phytoplankton pigments in surface sediments generally did not follow their dynamics in the water column, possibly due to intensive resuspension and a high sedimentation rate in a large and shallow lake. It was noticed that the surface sediment carries information on pigment degradation intensity and on weight and size characteristics of phytoplankton cells, which affect their sinking and floating velocities. Higher pigment contents of sediment in spring were presumably caused by lower resuspension due to high water level and slower degradation in cold water. Pheophytin a and the marker pigments of cyanobacteria were found to be persistent against degradation in upper sediment layers, which makes them useful indicators for tracking the historical changes in phytoplankton communities also in a shallow lake. Sharp decrease in chemically unstable pigment contents between the sediment surface and deeper layers indicates that only the uppermost sediment surface is resuspended in Lake Võrtsjärv. The transformation of the diatom marker carotenoid diadinoxanthin to diatoxanthin was found to occur mainly in sediments and not in the water column, and the

  4. Iron Isotope Fractionation Reveals Structural Change upon Microbial and Chemical Reduction of Nontronite NAu-1

    Science.gov (United States)

    Liu, K.; Wu, L.; Shi, B.; Smeaton, C. M.; Li, W.; Beard, B. L.; Johnson, C.; Roden, E. E.; Van Cappellen, P.

    2015-12-01

    Iron (Fe) isotope fractionations were determined during reduction of structural Fe(III) in nontronite NAu-1 biologically by Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA and chemically by dithionite. ~10% reduction was achieved in biological reactors, with similar reduction extents obtained by dithionite. We hypothesize that two stages occurred in our reactors. Firstly, reduction started from edge sites of clays and the produced Fe(II) partially remained in situ and partially was released into solution. Next aqueous Fe(II) adsorbed onto basal planes. The basal sorbed Fe(II) then undergoes electron transfer and atom exchange (ETAE) with octahedral Fe(III) in clays, with the most negative fractionation factor Δ56Febasal Fe(II)-structural Fe(III)of -1.7‰ when basal sorption reached a threshold value. Secondly, when the most reactive Fe(III) was exhausted, bioreduction significantly slowed down and chemical reduction was able to achieve 24% due to diffusion of small size dithionite. Importantly, no ETAE occurred between basal Fe(II) and structural Fe(III) due to blockage of pathways by collapsed clay layers. This two-stage process in our reduction experiments is distinctive from abiotic exchange experiments by mixing aqueous Fe(II) and NAu-1, where no structural change of clay would block ETAE between basal Fe(II) and structural Fe(III). The separation of reduction sites (clay edges) and sorption sites (basal planes) is unique to clay minerals with layered structure. In contrast, reduction and sorption occur on the same sites on the surfaces of Fe oxyhydroxides, where reduction does not induce structure change. Thus, the Fe isotope fractionations are the same for reduction and abiotic exchange experiments for Fe oxides. Our study reveals important changes in electron transfer and atom exchange pathways upon reduction of clay minerals by dissimilatory Fe reducing bacteria, which is prevalent in anoxic soils and sediments.

  5. Surface structure and biomedical properties of chemically polished and electropolished NiTi shape memory alloys

    Energy Technology Data Exchange (ETDEWEB)

    Chu, C.L. [School of Materials Science and Engineering, Southeast University, Nanjing, 211189 (China)], E-mail: clchu@seu.edu.cn; Wang, R.M. [School of Materials Science and Engineering, Southeast University, Nanjing, 211189 (China); Hu, T. [School of Materials Science and Engineering, Southeast University, Nanjing, 211189 (China); Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China); Yin, L.H.; Pu, Y.P. [School of Public Health, Southeast University, Nanjing 210096 (China); Lin, P.H. [School of Materials Science and Engineering, Southeast University, Nanjing, 211189 (China); Wu, S.L.; Chung, C.Y.; Yeung, K.W.K.; Chu, Paul K. [Department of Physics and Materials Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong (China)

    2008-12-01

    The surface structure and biomedical properties of NiTi shape memory alloy (SMA) samples after undergoing electropolishing and chemical polishing are determined and compared employing scanning electron microscopy, X-ray photoelectron spectroscopy, inductively-coupled plasma mass spectrometry, hemolysis analysis, blood platelet adhesion test, and MTT test. The results indicate that after chemical polishing, there is still a high Ni concentration on the surface of the NiTi SMA. On the other hand, electropolishing can form a thin surface titanium oxide film (about 10 nm thickness) with depleted Ni. In addition to the TiO{sub 2} phase, some titanium suboxides (TiO and Ti{sub 2}O{sub 3}) are found in the surface film. Compared to chemical polishing, electropolishing can more effectively mitigate out-diffusion of Ni ions and the wettability, blood compatibility, and thromboresistance are also better. However, no difference on the cytocompatibility can be observed from samples that have been chemically polished or electropolished.

  6. 75 FR 29718 - Carbazole Violet Pigment 23 From India and the People's Republic of China: Continuation of...

    Science.gov (United States)

    2010-05-27

    ... of Sales at Less Than Fair Value and Antidumping Duty Order: Carbazole Violet Pigment 23 From India...-proprietary information. In this case, the brackets are simply part of the chemical nomenclature....

  7. The influence of condensed tannin structure on rate of microbial mineralization and reactivity to chemical assays.

    Science.gov (United States)

    Norris, Charlotte E; Preston, Caroline M; Hogg, Karen E; Titus, Brian D

    2011-03-01

    We examined how tannin structure influences reactivity in tannin assays and carbon and nitrogen mineralization. Condensed tannins from the foliage of ten tree and shrub species and from pecan shells (Carya illinoensis) had different proportions of: (a) epicatechin (cis) and catechin (trans) isomers, (b) procyanidin (PC) and prodelphinidin (PD) monomers, and (c) different chain lengths. The response of each tannin to several widely used tannin assays was determined. Although there was some variation in response to proanthocyanidin (butanol/HCl) and Folin Ciocalteu assays, we did not deduce any predictable relationship between tannin structure and response to either assay. There was little variation in protein precipitation among the different tannins. To assess biological activity, six of the tannins were incubated with forest humus for 22 days. We determined that, while PC-based tannins remained at least partly extractable for the duration of the incubation, tannins with a high proportion of PD subunits rapidly became unextractable from soil. There was a positive correlation between net nitrogen mineralization and cis chemical structure. Carbon mineralization was enhanced initially by the addition of tannins to humus, but after 22 days, a negative correlation between the proportion of cis subunits and respiration was determined. Overall, we were not able to demonstrate consistent effects of structure on either microbial mineralization or reactivity to chemical assays; such relationships remain elusive.

  8. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    Science.gov (United States)

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (Ea), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. Ea, k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  9. Aged nano-structured platinum based catalyst: effect of chemical treatment on adsorption and catalytic activity.

    Science.gov (United States)

    Shim, Wang Geun; Nahm, Seung Won; Park, Hyuk Ryeol; Yun, Hyung Sun; Seo, Seong Gyu; Kim, Sang Chai

    2011-02-01

    To examine the effect of chemical treatment on the adsorption and catalytic activity of nanostructured platinum based catalyst, the aged commercial Pt/AC catalyst was pretreated with sulfuric acid (H2SO4) and a cleaning agent (Hexane). Several reliable methods such as nitrogen adsorption, X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and inductively coupled plasma (ICP) were employed to characterize the aged Pt/AC catalyst and its chemically pretreated Pt/AC catalysts. The catalytic and adsorption activities of nano-structured heterogeneous Pt/AC catalyst were investigated on the basis of toluene oxidation and adsorption isotherm data. In addition, the adsorption isotherms of toluene were used to calculate the adsorption energy distribution functions for the parent catalyst and its pre-treated nano-structured Pt/AC catalysts. It was found that sulfuric acid aqueous treatment can enhance the catalytic performance of aged Pt/AC catalyst toward catalytic oxidation of toluene. It was also shown that a comparative analysis of the energy distribution functions for nano-structured Pt/AC catalysts as well as the pore size distribution provides valuable information about their structural and energetic heterogeneity.

  10. Light-induced mutagenicity in Salmonella TA102 and genotoxicity/cytotoxicity in human T-cells by 3,3'-dichlorobenzidine: a chemical used in the manufacture of dyes and pigments and in tattoo inks.

    Science.gov (United States)

    Wang, Lei; Yan, Jian; Hardy, William; Mosley, Charity; Wang, Shuguang; Yu, Hongtao

    2005-02-28

    DCB, 3,3'-dichlorobenzidine, is used primarily as an intermediate in the manufacture of diarylide yellow or azo red pigments for printing ink, textile, paint, and plastics. It is also used in tattoo inks. In this article, we investigate light-induced toxicity of DCB in both bacteria and human Jurkat T-cells. DCB itself is not toxic or mutagenic to Salmonella typhimurium TA102, but is photomutagenic at concentrations as low as 2 microM and phototoxic at concentrations >100 microM when bacteria are exposed to DCB and light at the same time (1.2 J/cm2 of UVA and 2.1 J/cm2 of visible light). Furthermore, DCB is both photocytotoxic and photogenotoxic to human Jurkat T-cells. Under a light irradiation dose of 2.3 J/cm2 of UVA and 4.2 J/cm2 of visible light, it causes the Jurkat T-cells to become nonviable in a DCB dose-dependent manner and the nonviable cells reaches 60% at DCB concentrations higher than 50 microM. At the same time, DNA fragmentation is observed for cells exposed to both DCB and light, determined by single cell gel electrophoresis (alkaline comet assay). As much as 5% (average) DNA fragmentation was observed when exposed to 200 microM DCB and light irradiation. This suggests that DCB can penetrate the cell membrane and enter the cell. Upon light activation, DCB in the cells can cause various cellular damages, leading to nonviable Jurkat T-cells. It appears, the nonviable cells are not caused solely by fragmentation of cellular DNA, but by other damages such as to proteins and cell membranes, or DNA alkylation. Therefore, persons exposed to DCB through environmental contamination or through tattoo piercing using DCB-containing inks must not only concern about its toxicity without exposing to light, but also its phototoxicity.

  11. Prediction of drug disposition on the basis of its chemical structure.

    Science.gov (United States)

    Stepensky, David

    2013-06-01

    The chemical structure of any drug determines its pharmacokinetics and pharmacodynamics. Detailed understanding of relationships between the drug chemical structure and individual disposition pathways (i.e., distribution and elimination) is required for efficient use of existing drugs and effective development of new drugs. Different approaches have been developed for this purpose, ranging from statistics-based quantitative structure-property (or structure-pharmacokinetic) relationships (QSPR) analysis to physiologically based pharmacokinetic (PBPK) models. This review critically analyzes currently available approaches for analysis and prediction of drug disposition on the basis of chemical structure. Models that can be used to predict different aspects of disposition are presented, including: (a) value of the individual pharmacokinetic parameter (e.g., clearance or volume of distribution), (b) efficiency of the specific disposition pathway (e.g., biliary drug excretion or cytochrome P450 3A4 metabolism), (c) accumulation in a specific organ or tissue (e.g., permeability of the placenta or accumulation in the brain), and (d) the whole-body disposition in the individual patients. Examples of presented pharmacological agents include "classical" low-molecular-weight compounds, biopharmaceuticals, and drugs encapsulated in specialized drug-delivery systems. The clinical efficiency of agents from all these groups can be suboptimal, because of inefficient permeability of the drug to the site of action and/or excessive accumulation in other organs and tissues. Therefore, robust and reliable approaches for chemical structure-based prediction of drug disposition are required to overcome these limitations. PBPK models are increasingly being used for prediction of drug disposition. These models can reflect the complex interplay of factors that determine drug disposition in a mechanistically correct fashion and can be combined with other approaches, for example QSPR

  12. Interactions of natural resins and pigments in works of art.

    Science.gov (United States)

    Poli, Tommaso; Piccirillo, Anna; Nervo, Marco; Chiantore, Oscar

    2017-10-01

    The degradation process involving the formation of metal soaps in drying oils is a well-known problem due to cations from pigments reacting with free fatty acids from the oil. The aggregation of these carboxylates in semi-crystalline structures can lead to eruptions through the paint layers and 'blooming' on the surface. In this work, the metal soaps formation in presence of natural resins has been assessed and studied by means of Fourier transform infrared spectroscopy with experiments concerning the ageing of drying oil and different natural resins (shellac, dammar and colophony) in the presence of common historic pigments (smalt, ochre, umber, azurite, lead white, zinc white and titanium white). Mixtures of resins and pigments have been exposed to photo-ageing in solar box up to 1000h, thermal ageing at 50°C up to 1100h and 6month of room conditions exposure as reference. The decrease in the intensity of the carbonyl band in the spectra, as well as the contemporary increase of the metal carboxylates (in the range from 1500 to 1650cm(-1)) absorption bands, were used as the main indicators of metal soap formation. It has been observed that some pigments, particularly zinc white and smalt, present a 'catalytic' effect favouring the simultaneous formation of associated oxalates. The formation of oxalates and different degradation products from natural resins in the presence of pigments is particularly important, as it deeply affects the removability of varnishes and, more generally, the cleaning processes. Moreover, it permanently modifies the interface between painting and varnish layers as well as the aesthetic aspects of the painted surfaces. The influence of natural resins reactivity with pigments and their role in the oxalate formation is an issue still unexplored. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. A large scale analysis of information-theoretic network complexity measures using chemical structures.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

  14. Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

    Science.gov (United States)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

    2014-05-01

    The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

  15. Network structural analysis using directed graph for chemical reaction analysis in weakly-ionized plasmas

    Science.gov (United States)

    Nobuto, Kyosuke; Mizui, Yasutaka; Miyagi, Shigeyuki; Sakai, Osamu; Murakami, Tomoyuki

    2016-09-01

    We visualize complicated chemical reaction systems in weakly-ionized plasmas by analysing network structure for chemical processes, and calculate some indexes by assuming interspecies relationships to be a network to clarify them. With the current social evolution, the mean size of general data which we can use in computers grows huge, and significance of the data analysis increases. The methods of the network analysis which we focus on in this study do not depend on a specific analysis target, but the field where it has been already applied is still limited. In this study, we analyse chemical reaction systems in plasmas for configuring the network structure. We visualize them by expressing a reaction system in a specific plasma by a directed graph and examine the indexes and the relations with the characteristic of the species in the reaction system. For example, in the methane plasma network, the centrality index reveals importance of CH3 in an influential position of species in the reaction. In addition, silane and atmospheric pressure plasmas can be also visualized in reaction networks, suggesting other characteristics in the centrality indexes.

  16. Effects of age and sex on the structural, chemical and technological characteristics of mule duck meat.

    Science.gov (United States)

    Baeza, E; Salichon, M R; Marche, G; Wacrenier, N; Dominguez, B; Culioli, J

    2000-07-01

    1. The aim of the study was to analyse the effect of age and sex on the chemical, structural and technological characteristics of mule duck meat. 2. Ten males and 10 females were weighed and slaughtered at 8, 10, 11, 12 and 13 weeks of age. Weight, pH value, colour, tenderness and juice loss of breast muscle were determined. 3. The activities of 3 enzymes (citrate synthase, beta-hydroxyacyl CoA dehydrogenase, lactate dehydrogenase) which indicate muscular metabolic activity were assayed. 4. Chemical composition (moisture, lipids, proteins, minerals, lipid and phospholipid classes, fatty acid composition) of breast muscle was analysed. 5. Fibre type, fibre type percentage and cross-sectional areas were determined using histochemistry and an image analysis system. 6. For growth performance and muscular structure, the ideal slaughter age of mule ducks is 10 weeks of age. Chemical and technological analysis indicated that muscular maturity in Pectoralis major was reached at 11 weeks of age, but, at this age, breast lipid content is high. Moreover, after 10 weeks of age, food costs rapidly increased. 7. Lastly, sexual dimorphism for body weight is minor. In this study, at any given age, no significant differences between males and females were shown. Thus, it is possible to rear both sexes together and to slaughter them at the same age.

  17. Electronic structure and chemical bonding in LaIrSi-type intermetallics

    Energy Technology Data Exchange (ETDEWEB)

    Matar, Samir F. [Bordeaux Univ., Pessac (France). CNRS; Poettgen, Rainer [Muenster Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Nakhl, Michel [Univ. Libanaise, Fanar (Lebanon). Ecole Doctorale Sciences et Technologies

    2017-05-01

    The cubic LaIrSi type has 23 representatives in aluminides, gallides, silicides, germanides, phosphides, and arsenides, all with a valence electron count of 16 or 17. The striking structural motif is a three-dimensional network of the transition metal (T) and p element (X) atoms with TX{sub 3/3} respectively XT{sub 3/3} coordination. Alkaline earth or rare earth atoms fill cavities within the polyanionic [TX]{sup δ-} networks. The present work presents a detailed theoretical study of chemical bonding in LaIrSi-type representatives, exemplarily for CaPtSi, BaIrP, BaAuGa, LaIrSi, CeRhSi, and CeIrSi. DFT-GGA-based electronic structure calculations show weakly metallic compounds with itinerant small magnitude DOSs at E{sub F} except for CeRhSi whose large Ce DOS at E{sub F} leads to a finite magnetization on Ce (0.73 μ{sub B}) and induced small moments of opposite sign on Rh and Si in a ferromagnetic ground state. The chemical bonding analyses show dominant bonding within the [TX]{sup δ-} polyanionic networks. Charge transfer magnitudes were found in accordance with the course of the electronegativites of the chemical constituents.

  18. Heterogeneity of Physico-Chemical Properties in Structured Soils and Its Consequences

    Institute of Scientific and Technical Information of China (English)

    E. JASINSKA; H. WETZEL; T. BAUMGARTL; R. HORN

    2006-01-01

    Structured soils are characterized by the presence of inter- and intra-aggregate pore systems and aggregates, which show varying chemical, physical, and biological properties depending on the aggregate type and land use system. How far these aspects also affect the ion exchange processes and to what extent the interaction between the carbon distribution and kind of organic substances affect the internal soil strength as well as hydraulic properties like wettability are still under discussion. Thus, the objective of this research was to clarify the effect of soil aggregation on physical and chemical properties of structured soils at two scales: homogenized material and single aggregates. Data obtained by sequentially peeling off soil aggregates layers revealed gradients in the chemical composition from the aggregate surface to the aggregatecore. In aggregates from long term untreated forest soils we found lower amounts of carbon in the external layer, while in arable soils the differentiation was not pronounced. However, soil aggregates originating from these sites exhibited a higher concentration of microbial activity in the outer aggregate layer and declined towards the interior. Furthermore,soil depth and the vegetation type affected the wettability. Aggregate strength depended on water suction and differences in tillage treatments.

  19. Structural properties of zinc oxide and titanium dioxide nanoparticles prepared by chemical vapor synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Akgul, Guvenc, E-mail: guvencakgul@gmail.com [Bor Vocational School, Nigde University, 51700 Nigde (Turkey); Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Akgul, Funda Aksoy [Physics Department, Nigde University, 51240 Nigde (Turkey); Attenkofer, Klaus [Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Winterer, Markus [Nanoparticle Process Technology, Department of Engineering Sciences, and Center for NanoIntegration Duisburg-Essen, CeNIDE, University of Duisburg-Essen (Germany)

    2013-03-25

    Highlights: ► Local structure determination of ZnO and TiO{sub 2} nanostructures by XANES and EXAFS. ► Zn K and Ti K absorption edge XANES investigations of nanopowder samples. ► Investigation of pre-edge peak features of TiO{sub 2} nanosamples. ► Obtaining of local structure parameters of nano ZnO and TiO{sub 2} using EXAFS. ► Good agreement of EXAFS results and crystal structure datas. -- Abstract: Transition metal (TM) oxides provide a wide range of functional materials especially when nanostructured. Titanium dioxide (TiO{sub 2}) and wurtzite type zinc oxide (ZnO) nanostructured materials were fabricated by chemical vapor synthesis (CVS). Crystal and local structures of the prepared nanosamples were ascertained using X-ray diffraction (XRD), X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) techniques. Based on the XRD data, a second phase(s) was not found in both samples. A single wurtzite and anatase type structures were observed in ZnO and TiO{sub 2} nanosamples, respectively. Ti K pre-edge features of XANES spectrum indicated the presence of sixfold coordinated Ti in TiO{sub 2} nanosamples. The results showed that CVS is quite useful method to produce high crystalline nanoparticles.

  20. Heat-Resistant Ceramic Pigments on the Base of Waste Vanadium Catalyst and Alumina

    Directory of Open Access Journals (Sweden)

    M. B. Sedelnikova

    2013-01-01

    Full Text Available Ceramic pigments on the base of technogenic silica-containing material—waste vanadium catalyst were obtained in this work. Corundum is identified along with the predominant mullite phase in the composition of pigments. The ions of nickel, chromium, and iron are embedded in the structure if the concentration of the corresponding oxide in the initial mixture does not exceed 10 wt.%. In this case, the oxide is not identified in a free form according to the results of X-ray diffraction analysis. Spinel CoAl2O4 is formed in cobalt pigments. The developed pigments keep the firing temperature up to 1200°C. The obtained pigments may be recommended for ceramic paints and colored glazes for building materials.

  1. Multiple Roles of Photosynthetic and Sunscreen Pigments in Cyanobacteria Focusing on the Oxidative Stress

    Directory of Open Access Journals (Sweden)

    Seiichi Matsugo

    2013-05-01

    Full Text Available Cyanobacteria have two types of sunscreen pigments, scytonemin and mycosporine-like amino acids (MAAs. These secondary metabolites are thought to play multiple roles against several environmental stresses such as UV radiation and desiccation. Not only the large molar absorption coefficients of these sunscreen pigments, but also their antioxidative properties may be necessary for the protection of biological molecules against the oxidative damages induced by UV radiation. The antioxidant activity and vitrification property of these pigments are thought to be requisite for the desiccation and rehydration processes in anhydrobiotes. In this review, the multiple roles of photosynthetic pigments and sunscreen pigments on stress resistance, especially from the viewpoint of their structures, biosynthetic pathway, and in vitro studies of their antioxidant activity, will be discussed.

  2. Potential health hazards of organic pigments and dyes used in the manufacture of paints and surface coatings. Appendix I: scientific basis for the proposed regulation of dyes derived from the chemical substances benzidine, 3,3'-dimethylbenzidine, and 3,3'-dimethoxybenzidine

    Energy Technology Data Exchange (ETDEWEB)

    Jenkins, C.L.

    1978-05-08

    The scientific bases for regulating dyes derived from benzidine, 3,3'-dimethylbenzidine, and 3,3'-dimethoxybenzidine are presented. Studies of these compounds have demonstrated that benzidine-type dyes undergo nearly complete cleavage to known potent human carcinogenic agents through several metabolic and biological pathways, that these metabolites are carcinogenic in human and animal studies, that the toxicity and carcinogenicity of benzidine-type dyes has been demonstrated in animals, and that there is a high incidence of bladder cancer among users of benzidine-type dyes. Industrial workers were at risk through the inhalation of dye dusts, absorption through skin exposure, and accidental ingestion. Industries involved included dye manufacture, textile finishing, leather working, and paper dyeing. Direct dyes sold for home and craft use that may contain benzidine type dyes were listed by brand name and company or distributor. Commercial trade names of dyes and pigments based on these chemical substances were listed. Chemical identification of benzidine type dyes was described. Alternatives to benzidine type dyes were suggested, and a history of legislative attempts to regulate benzidine type dye production was provided.

  3. YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

    Energy Technology Data Exchange (ETDEWEB)

    Matar, S.F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France); Nakhl, M. [Universite Libanaise, Laboratoire de Chimie-Physique des Materiaux LCPM, Fanar (Lebanon); Al Alam, A.F.; Ouaini, N. [Universite Saint-Esprit de Kaslik, Faculte des Sciences et de Genie Informatique, Jounieh (Lebanon); Chevalier, B. [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France)

    2010-11-25

    Graphical abstract: Base centered orthorhombic YNiH{sub X} structure. For x = 3, only H1 and H2 are present. Highest hydrogen content YNiH{sub 4} is obtained when H3 are added. - Abstract: Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH{sub 3} and YNiH{sub 4} hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni-H bonding versus Y-H.

  4. Study of the chemical structure of petroleum asphaltenes by spectral methods

    Energy Technology Data Exchange (ETDEWEB)

    Posadov, I.A.; Pokonova, Yu.V.; Khusidman, M.B.; Gitlin, I.G.; Proskuryakov, V.A.

    1977-03-01

    Results of nuclear magnetic resonance (NMR), ultraviolet (UV), and infrared (IR) spectroscopy studies of the chemical and supermolecular structure of asphaltene concentrates isolated from petroleum residues are reported. Considerable intensity of a characteristic series of absorption bands at 750, 810, 870, 1560, 1600, and 3030 cm/sup -1/ is interpreted as indicative of aromatic structures; while the bands at 870 and 810 cm/sup -1/ are taken as evidence of the predominant presence of highly substituted aromatic rings which are apparently included in alicyclic structures but do not form polynuclear condensed aromatic systems. The bathochromic shift of the electronic absorption spectrum in the region of 250-600 nm and the weak inflection at 300-310 nm are attributed to the partial condensation of the aromatic rings with predominance of fragments of the bi- and tricyclic types. The percentage content of various organic groups, the degree of polycondensation, the degree of potential for substitution, and the elementary composition are reported.

  5. Isolation of peridininol, an anti-spasmodic carotenoid pigment, from Zoanthus sp.

    Digital Repository Service at National Institute of Oceanography (India)

    Parameswaran, P.S.; Achuthankutty, C.T.

    A C37 carotenoid pigment, peridininol, isolated from a marine Zoanthus sp. exhibited promising anti-spasmodic activity against nicotine and serotonin in in vitro studies using guinea pig ileum. Its purification and structure are presented along...

  6. Cribrarione B, a new naphthoquinone pigment from the myxomycete Cribraria cancellata.

    Science.gov (United States)

    Iwata, Dai; Ishibashi, Masami; Yamamoto, Yukinori

    2003-12-01

    Cribrarione B (1), a new naphthoquinone pigment, has been isolated from the myxomycete Cribrariacancellata, and its structure was elucidated as 2,5,8-trihydroxy-6-(1-hydroxyethyl)-[1,4]-naphthoquinone by NMR and mass spectral data.

  7. DRUGS CAUSING OROFACIAL PIGMENTATION: AN OVERVIEW OF LITERATURE

    OpenAIRE

    Shamimul Hasan; Nabeel Ishrat Khan; Osama Adeel Khan Sherwani; Shane Rafi; Ayesha Siddiqui

    2013-01-01

    The term “Oro-facial pigmentation” refers to a wide range of lesions or conditions featuring a change of color of Oro-facial tissues. Pigmentation of the Oro-facial tissues is seen in certain races or ethnic groups such as Indians, Africans and Europeans. Broadly classifying, Oro-facial pigmentation is divided into endogenous pigmentation and exogenous pigmentation. Endogenous pigmentation is due to pigments produced within the body. Exogenous pigmentation occurs when foreign bodies get impre...

  8. Structure and chemical characteristics of natural mineral deposit Terbunskaya (Lipetsk region, Russia)

    Energy Technology Data Exchange (ETDEWEB)

    Motyleva, S., E-mail: motyleva-svetlana@mail.ru; Mertvishcheva, M. [All-Russian Horticular Institute for Breeding, Agrotechnology and Nursery Russian Academy of Agricultural Sciences, Moskow (Russian Federation); Shchuchka, R.; Gulidova, V. [Yelets state university named after I. A. Bunin, Yelets (Russian Federation)

    2015-07-22

    New knowledge about the mineralogical features Terbunsky mineral. Investigated 5 fractions isolated from the incision (2-2,5 m). Terbunskaya deposit belongs to minerals Santonian age. Scanning electron microscopy and energy dispersive analysis of fractions isolated studied in detail. In the coarse fractions found ancient organic remains of algae and micro-organisms that have been sedimented together with the mineral component during geological periods. The share of organic inclusions does not exceed 1.5%. Chemical composition confirms the presence of silicon and carbonate organisms. Advantageously proportion of minerals having a layered structure with a plurality of micro and nano pore size 600 - 80-nm and an average chemical composition (wt%): Na (0,64), Mg (0,54), Al (13.48), Si (27 57), K (2.39) Ca (0.75)

  9. Structural, Mechanical and Optical Properties of Plasma-chemical Si-C-N Films

    Directory of Open Access Journals (Sweden)

    A.O. Kozak

    2014-11-01

    Full Text Available An influence of the substrate temperature in the range of 40-400 °C on the properties of the Si-C-N films deposited by plasma enhanced chemical vapor deposition (PECVD technique using hexamethyldisilazane is analyzed. Study of the structure, chemical bonding, surface morphology, mechanical properties and energy gap of the obtained films was carried out using X-ray diffraction, infrared spectroscopy, X-ray photoelectron spectroscopy, atomic force microscopy, optical measurements and nanoindentation. It was established that all the films were X-ray amorphous and had low surface roughness. Intensive hydrogen effusion from the films takes place, when substrate temperature increases up to 400 °C, which promotes a decrease of roughness and an increase in hardness and Young modules more than twice.

  10. Structural, chemical and magnetic properties of secondary phases in Co-doped ZnO

    Energy Technology Data Exchange (ETDEWEB)

    Ney, A; Ney, V; Ye, S; Ollefs, K; Kammermeier, T [Fakultaet fuer Physik and CeNIDE, Universitaet Duisburg-Essen, Lotharstrasse 1, D-47057 Duisburg (Germany); Kovacs, A; Dunin-Borkowski, R E [Center for Electron Nanoscopy, Technical University of Denmark, DK-2800 Kgs Lyngby (Denmark); Wilhelm, F; Rogalev, A, E-mail: andreas.ney@uni-due.de [European Synchrotron Radiation Facility (ESRF), 6 Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex (France)

    2011-10-15

    We have utilized a comprehensive set of experimental techniques such as transmission electron microscopy (TEM) and synchrotron-based x-ray absorption spectroscopy (XAS) and the respective x-ray linear dichroism and x-ray magnetic circular dichroism to characterize the correlation of structural, chemical and magnetic properties of Co-doped ZnO samples. It can be established on a quantitative basis that the superparamagnetic (SPM) behavior observed by integral superconducting quantum interference device magnetometry is not an intrinsic property of the material but stems from precipitations of metallic Co. Their presence is revealed by TEM as well as XAS. Annealing procedures for these SPM samples were also studied, and the observed changes in the magnetic properties found to be due to a chemical reduction or oxidation of the metallic Co species. (paper)

  11. On the Comparability of Chemical Structure and Roughness of Nanochannels in Altering Fluid Slippage

    CERN Document Server

    Misra, Chinmay Anand

    2016-01-01

    Interfacial hydrodynamic slippage of water depends on both on surface chemistry and roughness. This study tries to connect the effect of chemical property and the physical structure of the surface on the interfacial slippage of water. By performing molecular dynamics simulations (MDS) of Couette flow of water molecules over a reduced Lennard-Jones (LJ) surface, the velocity profile is obtained and extrapolated to get the slip lengths. The slip lengths are measured for various surface-fluid interactions. These interactions are varied by changing the wettability of the surface (characterized by the static contact angle) and its roughness. The slip length variation with the static contact angle as $(1+cos\\theta)^{-2}$ is observed. However, it is also observed that the presence of surface roughness always reduces the slip length and it is proposed that the slip length varies with non-dimensionalized average surface roughness as $(1+\\alpha^*)^{-2}$ . Thus a relation between the chemical wettability and the physica...

  12. Picobiophotonics for the investigation of pigment-pigment and pigment-protein interactions in photosynthetic complexes

    OpenAIRE

    Schmitt, Franz-Josef

    2011-01-01

    Anregungsenergietransfer-(EET)-prozesse wurden in verschiedenen photosynthetischen Pigment-Protein-Komplexen mit zeit- und wellenlängenkorrelierter Einzelphotonenspektroskopie (TWCSPC) analysiert. Ein neuer mobiler 16-Kanal Photomultiplier mit flexibler Faseroptik, austauschbaren Lichtquellen und einem Kryostaten (10 K – 350 K) wurde für die Spektroskopie von Proben in Küvetten, auf Oberflächen oder von ganzen Blättern in vivo aufgebaut. Das System stellt einen mobilen Messplatz auf Grundlage...

  13. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

    Directory of Open Access Journals (Sweden)

    Lotta Berg

    Full Text Available Acetylcholinesterase (AChE is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia to treat cholinergic deficiencies (e.g. in Alzheimer's disease, but may also act as dangerous toxins (e.g. nerve agents such as sarin. Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS. Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical

  14. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    Energy Technology Data Exchange (ETDEWEB)

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  15. In situ characterization of ancient plaster and pigments on tomb walls in Egypt using energy dispersive X-ray diffraction and fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Uda, M. E-mail: muda@waseda.jp

    2004-11-01

    A portable type of energy dispersive X-ray diffraction and fluorescence (ED-XRDF) spectrometer was developed, whose operation mode is completely different from that of an X-ray diffractometer commercially available. The former is operated in energy dispersive mode but the latter in angle dispersive mode. The performance of the ED-XRDF spectrometer was tested in the field, i.e. in the tomb of Amenhotep III, built in 1364 B.C. or earlier in Egypt. The crystal structure and chemical composition of ancient plaster and pigments were successfully determined in the field using the spectrometer. The same areas investigated by the ED-XRDF spectrometer were also examined with an optical microscope. The plaster is found to be composed of anhydrite, calcite and quartz. White and yellow pigments were identified as huntite and orpiment, respectively. Egyptian blue and goethite were found in the green colored parts.

  16. Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

    Directory of Open Access Journals (Sweden)

    Monika Batke

    2016-09-01

    Full Text Available 1.AbstractInterest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g. the European Union´s Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (<5. We discuss

  17. Chemical tagging can work: Identification of stellar phase-space structures purely by chemical-abundance similarity

    CERN Document Server

    Hogg, David W; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel

    2016-01-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were in fact born together (in the same molecular cloud), long ago. This idea has not previously yielded scientific successes, probably because of the noise and incompleteness in chemical-abundance measurements. However, we have succeeded in substantially improving spectroscopic measurements with The Cannon, which has delivered 15 individual abundances for 100,000 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are...

  18. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Microencapsulation by spray-drying of anthocyanin pigments from Corozo ( Bactris guineensis) fruit.

    Science.gov (United States)

    Osorio, Coralia; Acevedo, Baudilio; Hillebrand, Silke; Carriazo, José; Winterhalter, Peter; Morales, Alicia Lucía

    2010-06-09

    The anthocyanins of Bactris guineensis fruit were isolated with the aid of high-speed countercurrent chromatography (HSCCC) and preparative HPLC, and their chemical structures were elucidated by using spectroscopic methods. Among the identified pigments, cyanidin-3-rutinoside and cyanidin-3-glucoside were characterized as major constituents (87.9%). Peonidin-3-rutinoside, peonidin-3-glucoside, cyanidin-3-(6-O-malonyl)glucoside, and cyanidin-3-sambubioside were present in minor amounts. Four anthocyanin ethanolic extracts (AEEs) were obtained by osmotic dehydration and Soxhlet extraction and physicochemically characterized. The composition of anthocyanins was monitored by HPLC-PDA. The extracts with the highest anthocyanin content were subjected to the spray-drying process with maltodextrin. The so-obtained spray-dried powders were analyzed by scanning electron microscopy (SEM) and found to consist of spherical particles <50 microm in size. The anthocyanin composition was similar to that of the fruit. The microencapsulated powders were analyzed by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC), revealing that they are quite stable until 100 degrees C. Storage stability tests of microcapsules showed that the release of anthocyanin pigments follows pseudo-first-order kinetics and that the process rate is increased by temperature and humidity. The most suitable conditions for storage were below 37 degrees C and <76% relative humidity, respectively.

  20. Effect of chemical composition and density of the pelvic structure in intracavitary brachytherapy dosimetry

    Science.gov (United States)

    Chávez-Aguilera, N.; Torres-García, E.; Mitsoura, E.

    2011-03-01

    High dose rate (HDR) and low dose rate (LDR) intracavitary brachytherapies dosimetry in clinical practice are typically performed by commercial treatment planning systems. However, these systems do not fully consider the heterogeneities present in the real structure of the patient. The aim of this work is to obtain isodose curves and surfaces around the usual array of sources used in LDR ( 137Cs) and HDR ( 192Ir) intracavitary brachytherapy by Monte Carlo simulation, considering the real anatomic structure, density and chemical composition of media and tissues from the female pelvic region. The structural information was obtained from computed tomography images in the DICOM format. A voxel phantom (VP) was developed to perform ionizing radiation transport, considering the gamma spectrum of 137Cs and 192Ir. The absorbed dose was computed within each voxel of 2×2×3 mm 3. Four materials were considered in the VP—air, fat, muscle tissue and bone; however, one material per voxel was defined. Results show and quantify the effect of density and chemical composition of the medium on the absorbed dose distribution. According to them, the treatment planning systems underestimate the absorbed dose by 8% approximately for both radionuclides. In a heterogeneous medium, the absorbed dose distribution of 192Ir is more irregular than that of 137Cs but spatially better defined.